WO2024042168A1

WO2024042168A1 - Novel rna-guided nucleases and nucleic acid targeting systems comprising such rna-guided nucleases

Info

Publication number: WO2024042168A1
Application number: PCT/EP2023/073242
Authority: WO
Inventors: Tyson David BOWEN; Lila Herk RIEBER
Original assignee: UCB Biopharma SRL
Priority date: 2022-08-26
Filing date: 2023-08-24
Publication date: 2024-02-29

Abstract

The present invention provides novel RNA-guided nuclease proteins and nucleic acid targeting system comprising such for cleaving and/or modifying the target nucleotide of interest.

Description

NOVEL RNA-GUIDED NUCLEASES AND NUCLEIC ACID TARGETING SYSTEMS COMPRISING SUCH RNA-GUIDED NUCLEASES [001] The present invention relates to novel RNA-guided nucleases (RGN) and nucleic acid targeting systems comprising such. BACKGROUND [002] Targeted genome editing or modification has been undergoing many changes in the past years since the discovery of novel technologies and systems. First systems relied on meganucleases, zinc finger fusion proteins or Transcription activator-like effector nucleases (TALENs), requiring the generation of chimeric nucleases with engineered, sequence- specific DNA-binding domains specific for each particular target sequence. RNA-guided nucleases (RGNs), such as the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated (Cas) proteins allow for the targeting of specific sequences by using a short RNA sequence that specifically hybridizes with a particular target sequence. Such CRISPR systems became popular and gained multiple uses in research, diagnostics and therapeutics due to the ease of production of target-specific short RNA sequences and use of such with the same RGN protein. Such RGNs can be used to edit genomes through the introduction of a sequence-specific, double -stranded break that is either repaired and introduces a mutation or repaired by introducing a stretch of heterologous DNA. Inactive versions RGNs has been also widely used to target specific DNA or RNA regions and in combination with other proteins allowed to study and modulate multiple cellular processes and provide a useful tool for gene function study and modulation of their activity. SUMMARY OF THE INVENTION [003] The present invention provides novel type Va RNA-guided nuclease (RGN) polypeptides, CRISPR RNAs (crRNAs), nucleic acid targeting systems comprising those, nucleic acid molecules encoding the same, and vectors and host cells comprising such nucleic acid molecules. [004] Also provided are nucleic acid targeting systems for binding a target nucleic acid sequence of interest, wherein the system comprises a RGN polypeptide and one or more RNA sequences targeting the nucleic acid of interest. [005] Thus, methods disclosed herein are drawn to binding a target sequence of interest, and in some embodiments, cleaving or modifying the target sequence of interest. The target sequence of interest can be modified, for example, as a result of non-homologous end joining or homology-directed repair with an introduced donor sequence. BRIEF DESCRIPTION OF THE DRAWINGS [006] The present invention is described below by reference to the following figures. 1 [007] Figure 1. PAM Accessibility. Addressable space of a theoretical genome with and even distribution of nucleotides for each PAM in this disclosure and compared to the PAM of AsCas12a (TTTV). The column of numbers indicates how much of the theoretical genome is addressable by the PAM of interest. [008] Figure 2 PAM Dependent Editing with Mutated Cas12a Variants. Shows the performance of several point mutations for Cas12a variants. Indel activity in 293T cells of EGS0068 at 25 targets (wildtype) or 31 targets (mutant), EGS0081 at 34 targets (wildtype) or 31 targets (mutant), and EGS0087 at 24 targets (wildtype) or 30 targets (mutant) with the indicated PAM sequence. Each dot represents a single target site, averaged from replicates. Paired t test comparisons were performed considering just identical target sites across systems. Median performance of all sites in the system is indicated with a horizontal bar. DETAILED DESCRIPTION OF THE INVENTION Definitions [009] Table 1. Abbreviations used throughout the specification

[010] Table 2. Amino acids abbreviations

2

[011] Table 3. Nucleotide abbreviations

[012] The following definitions are used throughout the description. [013] The term "adeno-associated virus" or "AAV" as used interchangeably herein refers to a small virus belonging to the genus Dependovirus of the Parvoviridae family that infects humans and some other primate species. AAV is not currently known to cause disease and consequently the virus causes a very mild immune response. [014] As used herein, a “biological sample” may contain whole cells and/or live cells and/or cell debris. The biological sample may contain (or be derived from) a “bodily fluid”. Bodily fluids may be obtained from a mammal organism, for example by puncture, or other collecting or sampling procedures. [015] The term “Cas12a” refers to type of an RGN that cleaves nucleic acid and is encoded by the CRISPR loci and is a part of the Type Va CRISPR system. The Cas12a protein commonly used is from bacterial species Acidaminococcus sp. The Cas12a protein may be mutated so that the nuclease activity is partly or completely inactivated. [016] The term “Cas9” refers to type of an RGN that cleaves nucleic acid and is encoded by the CRISPR loci and is a part of the Type II CRISPR system. The Cas9 protein commonly used is from bacterial species Streptococcus pyogenes. The Cas9 protein may be mutated so that the nuclease activity is partly or completely inactivated. [017] The term "complement" or "complementary" as used herein means a nucleic acid can mean Watson-Crick or Hoogsteen base pairing between nucleotides or nucleotide analogs of nucleic acid molecules. The term "complementarity" refers to a property shared between two nucleic acid 3

sequences, such that when they are aligned antiparallel to each other, the nucleotide bases at each position will be complementary. [018] The term “CRISPR” (Clustered Regularly Interspaced Short Palindromic Repeats) refers to a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea. These sequences are derived from DNA fragments of bacteriophages that had previously infected the prokaryote. They are used to detect and destroy DNA from similar bacteriophages during subsequent infections. [019] The term "CRISPR system" refers collectively to transcripts and other elements involved in the expression of or directing the activity of CRISPR-associated ("Cas") proteins, including sequences encoding a Cas protein, a tracr (trans -activating CRISPR) sequence (e.g. tracrRNA or an active partial tracrRNA), a tracr-mate sequence (containing a "direct repeat" and a tracrRNA-processed partial direct repeat in the context of an endogenous CRISPR system), a guide sequence (also referred herein to as a "spacer" in the context of an endogenous CRISPR system), or other sequences and transcripts from a CRISPR locus. [020] The term “crRNA” refers to a nucleotide sequence having sufficient complementarity with a target nucleotide sequence to hybridize with the target sequence and direct sequence-specific binding of an associated RNA- guided nuclease to the target nucleotide sequence. [021] The term “effective amount,” as used herein, refers to an amount of a biologically active agent that is sufficient to elicit a desired biological response. For example, in some embodiments, an effective amount of a nuclease may refer to the amount of the nuclease that is sufficient to induce cleavage of a target site specifically bound and cleaved by the nuclease. In some embodiments, an effective amount of a recombinase may refer to the amount of the recombinase that is sufficient to induce recombination at a target site specifically bound and recombined by the recombinase. As will be appreciated by the skilled artisan, the effective amount of an agent, e.g., a nuclease, a recombinase, a hybrid protein, a fusion protein, a protein dimer, a complex of a protein (or protein dimer) and a polynucleotide, or a polynucleotide, may vary depending on various factors as, for example, on the desired biological response, the specific allele, genome, target site, cell, or tissue being targeted, and the agent being used. [022] The term "enhancer" as used herein refers to non-coding DNA sequences containing multiple activator and repressor binding sites. Enhancers range from 200 bp to 1 kb in length and may be either proximal, 5' upstream to the promoter or within the first intron of the regulated gene, or distal, in introns of neighboring genes or intergenic regions far away from the locus. Through DNA looping, active enhancers contact the promoter dependently of the core DNA binding motif promoter specificity.4 to 5 enhancers may interact with a promoter. 4

[023] As used herein, the term "fusion protein" refers to a chimeric protein created through the covalent or non-covalent joining of two or more genes, directly or indirectly, that originally coded for separate proteins. In some embodiments, the translation of the fusion gene results in a single polypeptide with functional properties derived from each of the original proteins. [024] The term “gRNA”, also used interchangeably herein as a chimeric single guide RNA (“sgRNA”), refers to nucleic acid which is a fusion of two noncoding RNAs: a crRNA and a tracrRNA. “gRNA” is used interchangeably to refer to guide RNAs that exist as either single molecules or as a complex of two or more molecules. Typically, gRNAs that exist as single RNA species comprise two domains:(1) a domain that shares homology to a target nucleic acid (e.g., and directs binding of a Cas9 complex to the target); and (2) a domain that binds a Cas9 protein. [025] An "isolated" or "purified" polypeptide, or biologically active portion thereof, is substantially or essentially free from components that normally accompany or interact with the polypeptide as found in its naturally occurring environment. Thus, an isolated or purified polypeptide is substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. A protein that is substantially free of cellular material includes preparations of protein having less than 30%, 20%, 10%, 5%, or 1% (by dry weight) of contaminating protein. When a protein or biologically active portion thereof is recombinantly produced, optimally culture medium represents less than 30%, 20%, 10%, 5%, or 1% (by dry weight) of chemical precursors or non-protein-of-interest chemicals. [026] The term “linker,” as used herein, refers to a chemical group or a molecule linking two molecules or moieties, e.g., a binding domain and a cleavage domain of a nuclease. Typically, the linker is positioned between, or flanked by, two groups, molecules, or other moieties and connected to each one via a covalent bond, thus connecting the two. In some embodiments, the linker is an amino acid or a plurality of amino acids (e.g., a peptide or protein). In some embodiments, the linker is an organic molecule, group, polymer, or chemical moiety. In some embodiments, the linker is a polypeptide of 5-100 amino acids in length, for example, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 30-35, 35-40, 40-45, 45-50, 50-60, 60-70, 70-80, 80- 90, 90-100, 100-150, or 150-200 amino acids in length. Longer or shorter linkers are also contemplated. [027] The term “modification” in reference to a nucleic acid molecule refers to a change in the nucleotide sequence of the nucleic acid molecule, which can be a deletion, insertion, or substitution of one or more nucleotides, or a combination thereof. [028] The term “mutation,” as used herein, refers to a substitution of a residue within a sequence, e.g., a nucleic acid or amino acid sequence, with another residue, or a deletion or insertion of one or more residues within a sequence. Mutations are typically described herein by identifying the original 5

residue followed by the position of the residue within the sequence and by the identity of the newly substituted residue. Various methods for making the amino acid substitutions (mutations) provided herein are well known in the art, and are provided by, for example, Green and Sambrook, Molecular Cloning: A Laboratory Manual (4th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2012)). [029] As used herein, the terms "nucleic acid," "nucleic acid sequence," "nucleotide sequence," "oligonucleotide," and "polynucleotide" are interchangeable and refer to a polymeric form of nucleotides. The nucleotides may be deoxyribonucleotides (DNA), ribonucleotides (RNA), analogs thereof, or combinations thereof, and may be of any length. Polynucleotides may perform any function and may have any secondary and tertiary structures. The terms encompass known analogs of natural nucleotides and nucleotides that are modified in the base, sugar and/or phosphate moieties. Analogs of a particular nucleotide have the same base-pairing specificity (e.g., an analog of A base pairs with T). A polynucleotide may comprise one modified nucleotide or multiple modified nucleotides. Examples of modified nucleotides include fluorinated nucleotides, methylated nucleotides, and nucleotide analogs. Nucleotide structure may be modified before or after a polymer is assembled. Following polymerization, polynucleotides may be additionally modified via, for example, conjugation with a labeling component or target binding component. A nucleotide sequence may incorporate non-nucleotide components. The terms also encompass nucleic acids comprising modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, and have similar binding properties as a reference polynucleotide (e.g., DNA or RNA). Examples of such analogs include, but are not limited to, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs), Locked Nucleic Acid (LNA™) (Exiqon, Inc., Woburn, MA) nucleosides, glycol nucleic acid, bridged nucleic acids, and morpholino structures. Polynucleotide sequences are displayed herein in the conventional 5' to 3' orientation unless otherwise indicated. [030] The term “operably linked” as used herein means that expression of a gene is under the control of a promoter with which it is spatially connected. A promoter may be positioned 5′ (upstream) or 3′ (downstream) of a gene under its control. The distance between the promoter and a gene may be approximately the same as the distance between that promoter and the gene it controls in the gene from which the promoter is derived. As is known in the art, variation in this distance may be accommodated without loss of promoter function. [031] The term “optional” or “optionally” means that the subsequent described event, circumstance or substituent may or may not occur, and that the description includes instances where the event or circumstance occurs and instances where it does not. 6

[032] As used herein, the terms "peptide," "polypeptide," and "protein" are interchangeable and refer to polymers of amino acids. A polypeptide may be of any length. It may be branched or linear, it may be interrupted by non-amino acids, and it may comprise modified amino acids. The terms may be used to refer to an amino acid polymer that has been modified through, for example, acetylation, disulfide bond formation, glycosylation, lipidation, phosphorylation, cross- linking, and/or conjugation (e.g., with a labeling component or ligand). Polypeptide sequences are displayed herein in the conventional N-terminal to C-terminal orientation. Polypeptides and polynucleotides can be made using routine techniques in the field of molecular biology (see, e.g., standard texts set forth above). Further, essentially any polypeptide or polynucleotide can be custom ordered from commercial sources. [033] As used herein, "percentage of sequence identity" means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i. e. , gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity. [034] The term "promoter" as used herein means a synthetic or naturally-derived molecule which is capable of conferring, activating or enhancing expression of a nucleic acid in a cell. A promoter may comprise one or more specific transcriptional regulatory sequences to further enhance expression and/or to alter the spatial expression and/or temporal expression of same. A promoter may also comprise distal enhancer or repressor elements, which may be located as much as several thousand base pairs from the start site of transcription. A promoter may be derived from sources including viral, bacterial, fungal, plants, insects, and animals. [035] The term “RNA-guided endonuclease” or “RGN” is used interchangeably herein and refer to a nuclease that forms a complex with (e.g., binds or associates with) one or more RNA that is not a target for cleavage. [036] As used herein, "sequence identity" or "identity" in the context of two polynucleotides or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window. When percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or 7

hydrophobicity) and therefore do not change the functional properties of the molecule. When sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. [037] Sequences that differ by such conservative substitutions are said to have "sequence similarity" or "similarity". Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g. , as implemented in the program PC/GENE (Intelligenetics, Mountain View, California). [038] As used herein the term “spacer sequence” or “spacer” refers to a part of lmntRNA nucleotide sequence that directly hybridizes with the target nucleotide sequence of interest. [039] The term "subject" and "patient" as used herein interchangeably refers to any vertebrate, including, but not limited to, a mammal {e.g., cow, pig, camel, llama, horse, goat, rabbit, sheep, hamsters, guinea pig, cat, dog, rat, and mouse, a non-human primate (for example, a monkey, such as a cynomolgus or rhesus monkey, chimpanzee, etc.) and a human). In some embodiments, the subject may be a human or a non-human. The subject or patient may be undergoing other forms of treatment. [040] The term “target region”, “target sequence” or “protospacer” as used interchangeably herein refers to the region of the target gene to which the CRISPR-based system targets. [041] The terms “treatment,” “treat,” and “treating,” refer to a clinical intervention aimed to reverse, alleviate, delay the onset of, or inhibit the progress of a disease or disorder, or one or more symptoms thereof, as described herein. As used herein, the terms “treatment,” “treat,” and “treating” refer to a clinical intervention aimed to reverse, alleviate, delay the onset of, or inhibit the progress of a disease or disorder, or one or more symptoms thereof, as described herein. In some embodiments, treatment may be administered after one or more symptoms have developed and/or after a disease has been diagnosed. In other embodiments, treatment may be administered in the absence of symptoms, e.g., to prevent or delay onset of a symptom or inhibit onset or progression of a disease. For example, treatment may be administered to a susceptible individual prior to the onset of symptoms (e.g., in light of a history of symptoms and/or in light of genetic or other susceptibility factors). Treatment may also be continued after symptoms have resolved, for example, to prevent or delay their recurrence [042] The term “Type II CRISPR system” refers to effector system that carries out targeted DNA double-strand break in four sequential steps, using a single effector enzyme, Cas9, to cleave dsDNA. Compared to the Type I and Type III effector systems, which require multiple distinct effectors acting as a complex, the Type II effector system may function in alternative contexts such as eukaryotic 8

cells. The Type II effector system consists of a long pre-crRNA, which is transcribed from the spacer- containing CRISPR locus, the Cas9 protein, and a tracrRNA, which is involved in pre-crRNA processing. [043] The term "vector" as used herein means a nucleic acid sequence containing an origin of replication. A vector may be a viral vector, bacteriophage, bacterial artificial chromosome or yeast artificial chromosome. A vector may be a DNA or RNA vector. A vector may be a self- replicating extrachromosomal vector, or a DNA plasmid. [044] Unless otherwise defined herein, scientific and technical terms used in connection with the present disclosure shall have the meanings that are commonly understood by those of ordinary skill in the art. CRISPR systems [045] The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) genomic locus is found in the genomes of many prokaryotes. CRISPR loci provide resistance to viruses and phages in prokaryotes. In this way, the CRISPR loci functions as a type of immune system to help defend prokaryotes against foreign invaders. In such system the response to such foreign invaders starts by cleaving the genome of invading viruses and plasmids and integrating segments (termed protospacers) of the genomic DNA into the CRISPR locus of the host organism. The segments that are integrated into the host genome are known as “spacers”, which mediate protection from subsequent attack by the same (or sufficiently related) virus or plasmid. Expression involves transcription of the CRISPR locus and subsequent enzymatic processing to produce short mature CRISPR RNAs (crRNA), each containing a single spacer sequence. Interference is induced after the CRISPR RNAs associate with Cas proteins to form effector complexes, which are then targeted to complementary protospacers in foreign genetic elements to induce nucleic acid degradation. [046] Currently, two classes of CRISPR systems have been described, Class 1 and Class 2, based upon the genes encoding the effector component. Class 1 systems have a multi-subunit crRNA- effector complex, whereas Class 2 systems have a single effector protein. Typical examples of Class 2 effector proteins are Cas9 and Cpf1 (Cas12a). [047] To date six types (Types I-VI) of CRISPR systems have been described (for an overview see Makarova et al., Nature Reviews Microbiology (2015) 13:1-15). Class 1 systems comprise Type I, Type III and Type IV systems. Class 2 systems comprise Type II, Type V and Type VI systems. [048] CRISPR loci include several short repeating sequences referred to as "repeats." The repeats can form hairpin structures and/or the repeats can be single-stranded sequences. The repeats occur in clusters. Repeats frequently diverge between species. Repeats are regularly interspaced with unique intervening sequences, referred to as "spacers," resulting in a repeat-spacer-repeat locus architecture. 9

Spacers are sequences usually identical to or homologous to foreign invader sequences (such as viral sequences). [049] In some cases, a spacer-repeat unit encodes a crisprRNA (crRNA). A crRNA refers to the mature form of the spacer-repeat unit. A crRNA contains a spacer sequence that is involved in targeting a target nucleic. crRNA has a region of complementarity to a potential DNA or RNA target sequence and in some cases, e.g., in currently characterized Type II systems, a second region that forms base-pair hydrogen bonds with a transactivating CRISPR RNA (tracrRNA) to form a secondary structure, typically to form at least a stem structure. Complex formation between tracrRNA/crRNA and a Cas protein results in conformational change of the Cas protein that facilitates binding to DNA, nuclease activities of the Cas protein, and crRNA- guided site-specific DNA cleavage by the nuclease. For a Cas protein/tracrRNA/crRNA complex to cleave a DNA target sequence, the DNA target sequence is adjacent to a cognate protospacer adjacent motif (PAM). [050] Usually, CRISPR locus comprises polynucleotide sequences encoding for CRISPR Associated Genes (cas) genes. Cas genes are involved in the biogenesis and/or the interference stages of crRNA function. Cas genes display extreme sequence diversity between different species and homologs. Some Cas proteins comprise a specific set of domain structures. [051] Mature crRNAs are processed from a longer polycistronic CRISPR locus transcript, also referred to as pre-crRNA array. A pre-crRNA array comprises a plurality of crRNAs. The repeats in the pre-crRNA array are recognized by cas genes. Cas genes bind to the repeats and cleave the repeats. This action can liberate the plurality of crRNAs. crRNAs can be subjected to further events to produce the mature crRNA form such as trimming (e.g., with an exonuclease). A crRNA may comprise all, or some, of the CRISPR repeat sequences. [052] Interference refers to the stage in the CRISPR system that is functionally responsible for combating infection by a foreign invader. CRISPR interference follows a similar mechanism to RNA interference, which results in target RNA degradation and/or destabilization. Currently characterized CRISPR systems perform interference of a target nucleic acid by coupling crRNAs and Cas genes, thereby forming CRISPR ribonucleoproteins (RNPs). crRNA of the RNP guides the RNP to foreign invader nucleic acid, (e.g. , by recognizing the foreign invader nucleic acid through hybridization). Hybridized target foreign invader nucleic acid- crRNA units are subjected to cleavage by Cas proteins. Target nucleic acid interference typically requires a protospacer adjacent motif (PAM) in a target nucleic acid. [053] Currently CRISPR-Cas systems are divided into two main classes based on their effector molecules: class 1 and class 2. Class 1 is characterized by multi-unit effector molecules, while class 2 contains a single effector molecule. Class 1 systems comprise Type I, Type III, and Type IV systems. Class 2 systems comprise Type II, Type V, and Type VI systems. 10

[054] Type II system is commonly represented by cas9 genes. There are two strands of RNA in Type II systems: a crRNA and a tracrRNA. The duplex formed by the tracrRNA and crRNA is recognized by, and associates with Cas9, encoded by the cas9 gene, which combines the functions of the crRNA- effector complex with target DNA cleavage. Cas9 is directed to a target nucleic acid by a sequence of the crRNA that is complementary to, and hybridizes with, a sequence in the target nucleic acid. [055] In Type V systems, nucleic acid target sequence binding involves a Cas12 protein and the crRNA, as does the nucleic acid target sequence cleavage. In Type V systems, the RuvC-like nuclease domain of Cas12 protein cleaves both strands of the nucleic acid target sequence in a sequential fashion (Swarts, et αΙ. , ΜοΙ. Cell (2017) 66:221 -233. e4), producing 5' overhangs, which differs from the fragments generated by Cas9 protein. There have been multiple subtypes of Type V systems identified so far (type V-A/B/C/D/E/F/G/H/I/K/L and CRISPR-Cas12j). All of them differ by the length of Cas protein, PAM sequence and whether they require tracrRNA for its functionality. [056] Type V-A is represented by Cas12a protein. The Cas12a protein cleavage activity of Type V-A systems does not require hybridization of crRNA to tracrRNA to form a duplex; rather Type V-A systems use a single crRNA that has a stem-loop structure forming an internal duplex. Cas12a protein binds the crRNA in a sequence- and structure-specific manner by recognizing the stem loop and sequences adjacent to the stem loop, most notably the nucleotides 5' of the spacer sequence, which hybridizes to the nucleic acid target sequence. This stem-loop structure is typically in the range of 15 to 22 nucleotides in length. Substitutions that disrupt this stem-loop duplex abolish cleavage activity, whereas other substitutions that do not disrupt the stem-loop duplex do not abolish cleavage activity. [057] In Type V-A systems, nucleic acid target sequence binding involves Cas12a and the crRNA, as does the nucleic acid target sequence cleavage. In Type V systems, the RuvC-like nuclease domain of Cas12a cleaves one strand of the double-stranded nucleic acid target sequence, and a putative nuclease domain cleaves the other strand of the double- stranded nucleic acid target sequence in a staggered configuration, producing 5' overhangs, which is different from the blunt ends generated by Cas9 cleavage. These 5' overhangs may facilitate insertion of DNA. [058] The Cas12a cleavage activity of Type V-A systems also does not require hybridization of crRNA to tracrRNA to form a duplex, rather the crRNA of Type V-A systems uses a single crRNA that has a stem-loop structure forming an internal duplex. Cas12a binds the crRNA in a sequence and structure specific manner that recognizes the stem loop and sequences adjacent to the stem loop, most notably the nucleotide 5' of the spacer sequences that hybridizes to the nucleic acid target sequence. This stem-loop structure is typically in the range of 15 to 22 nucleotides in length. Substitutions that disrupt this stem-loop duplex abolish cleavage activity, whereas other substitutions that do not disrupt the stem-loop duplex do not abolish cleavage activity. In Type V systems, the crRNA forms a stem- loop structure at the 5 ' end, and the sequence at the 3' end is complementary to a sequence in a nucleic acid target sequence. 11

[059] Other proteins associated with Type V crRNA and nucleic acid target sequence binding and cleavage include Cas12b, Cas12c, Cas12d, and Cas12e which are similar in length to Cas12a proteins, ranging from approximately 1000-1500 amino acids, but also require an additional RNA (either a tracRNA or a scoutRNA, see e.g. Harrington, L., et al, Molecular Cell, Volume 79, Issue 3, 2020,Pages 416-424). Still other proteins associated with Type V crRNA and nucleic acid target sequence binding and cleavage include Cas12f1, Cas12f2, Cas12f3, and Cas12g, which are smaller in length to Cas12a proteins, ranging from approximately 300-900 amino acids, but also require a tracrRNA. [060] Type VI systems include the Cas13a protein (also known as Class 2 candidate 2 protein, or C2c2) which does not share sequence similarity with other CRISPR effector proteins (see Abudayyeh, et al, Science (2016) 353:aaf5573). Cas13a proteins have two HEPN domains and possess single- stranded RNA cleavage activity. Cas13a proteins are similar to Cas12a proteins in requiring a crRNA for nucleic acid target sequence binding and cleavage, but not requiring tracrRNA. [061] While many of type V systems have been identified, the discovery and characterization of CRISPR systems and individual Cas proteins is ongoing. RNA-guided nucleases (RGNs) [062] The present disclosure provides novel RNA-guided nucleases (RGN) as defined by their amino acid sequences in Table 4. The inventors have identified and tested multiple RGN proteins of class V- A in both procaryotic and eucaryotic cells and have identified that only a part of them did function in both cell types. Those are provided in Table 4. These systems exhibit a large diversity of PAM sequences, enabling greater, and more flexible targeting space. Additionally, as the systems are derived from a variety of sources, they will be better suited for in vivo editing where pre-existing antibodies to other Cas12a proteins (either naturally occurring or from previous treatment) prevent effective use.( see e.g. Simhadri, et al (2018) Molecular therapy. Methods & clinical development, 10, 105–112). The RGN polypeptides provided herein share very limited sequence similarity to known Cas12a proteins. [063] Table 4 Novel RGNs

12

[064] An RNA-guided nuclease provided herein binds to a target nucleotide sequence and hybridizes with the crRNA molecule specific to the RNA-guided nuclease. The target sequence can then be subsequently cleaved by the RGN if the RGN polypeptide possesses nuclease activity. The presently disclosed RGNs can cleave nucleotides within a polynucleotide, functioning as an endonuclease. In some embodiments, the disclosed RGNs can cleave nucleotides of a target nucleotide sequence within any position of a polynucleotide and thus function as both an endonuclease and exonuclease. [065] The presently disclosed RGNs can be wild-type sequences derived from bacterial or archaeal species. Alternatively, the RGNs can be variants or fragments of wild-type polypeptides. The wild- type RGN can be modified to alter nuclease activity or alter PAM specificity, for example. In some embodiments, the RGN is not naturally-occurring. [066] In other embodiments, the RGNs lacks nuclease activity altogether or exhibits reduced nuclease activity and is referred to herein as nuclease-dead RGNs. Any method known in the art for introducing mutations into an amino acid sequence, such as PCR-mediated mutagenesis and site- directed mutagenesis, can be used for generating nickases or nuclease-dead RGNs. (e.g. US2014/0068797 and US9,790,490). [067] Alternatively, nuclease dead RGNs can be targeted to particular genomic locations to alter the expression of a desired sequence. In some embodiments, the binding of a nuclease-dead RNA-guided 13

nuclease to a target sequence results in the repression of expression of the target sequence or a gene under transcriptional control by the target sequence by interfering with the binding of RNA polymerase or transcription factors within the targeted genomic region. In other embodiments, the RGN (e.g., a nuclease- dead RGN) or its complexed guide RNA further comprises an expression modulator that, upon binding to a target sequence, serves to either repress or activate the expression of the target sequence or a gene under transcriptional control by the target sequence. In some of these embodiments, the expression modulator modulates the expression of the target sequence or regulated gene through epigenetic mechanisms. [068] In other embodiments, the nuclease-dead RGNs or a RGN with only nickase activity can be targeted to particular genomic locations to modify the sequence of a target polynucleotide through fusion to a base editing polypeptide, for example a deaminase polypeptide or active variant or fragment thereof that deaminates a nucleotide base, resulting in conversion from one nucleotide base to another. The base-editing polypeptide can be fused to the RGN at its N-terminal or C-terminal end. Additionally, the base-editing polypeptide may be fused to the RGN via a peptide linker. A non- limiting example of a deaminase polypeptide that is useful for such compositions and methods include cytidine deaminase or the adenosine deaminase base editor described in Gaudelli et al. (2017) Nature 551:464-471, and WO2018/027078. Structural elements of the RGN peptides [069] Naturally occurring type-V effectors employ multiple domains distributed in a recognition lobe (REC) and a nuclease lobe (NUC) for substrate recognition and cleavage. In some embodiments the REC lobe of RGN peptides provided herein consists of a WED-I, REC1, and REC2 domains, where as the NUC lob consists of a WED-II, PAM Interacting (PI), WED-III, and a Tris-split RuvC domain. RuvC domain [070] The RuvC domain may comprise multiple subdomains: RuvC-I, RuvC-II and RuvC-III. The subdomains may be separated by other sequences on the amino acid sequence of the protein. [071] Examples of RuvC domains include any polypeptides having a structural similarity and/or sequence similarity to a RuvC domain described in the art. For example, the RuvC domain may share a structural similarity and/or sequence similarity to a RuvC of Cas9. In some examples, the RuvC domain may have an amino acid sequence that share at least 80%, at least 85%, at least 90%, at least 95%, at least 99%, or 100% sequence identity with RuvC domains. [072] In some examples, the RuvC domain comprise RuvC-I polypeptide, RuvC-II polypeptide, and RuvC-III polypeptide. Examples of the RuvC-I domain also include any polypeptides having a structural similarity and/or sequence similarity to a RuvC-I, II, and III domains described in the art, such as the corresponding domains of Cas9. The RuvC domain may have an amino acid sequence that 14

share at least 80%, at least 85%, at least 90%, at least 95%, at least 99%, or 100% sequence identity with a RuvC domain of Cas9. [073] The RuvC domain of Cas9 consists of a six-stranded mixed P-sheet flanked by a-helices and two additional two-stranded antiparallel P-sheets (see e.g., Nishimasu et al. Cell, 2014). The RuvC domain of Cas9 shares structural similarity with the retroviral integrase superfamily members characterized by an RNase H fold, such as Escherichia coli RuvC (PDB code 1HJR, 14% identity, root-mean-square deviation (rmsd) of 3.6 A for 126 equivalent Ca atoms) and Thermus thermophilus RuvC (PDB code 4LD0, 12% identity, rmsd of 3.4 A for 131 equivalent Ca atoms). E. coli RuvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices. RuvC nucleases have four catalytic residues (e.g., Asp7, Glu70, Hisl43 and Aspl46 in T. thermophilus RuvC), and cleave Holliday junctions (or structurally analogous cruciform junctions) through a two- metal mechanism. Asp 10 (Ala), Glu762, His983 and Asp986 of the Cas9 RuvC domain are located at positions similar to those of the catalytic residues of T. thermophilus RuvC. REC domain [074] The REC domain may comprise multiple subdomains: REC1 and REC2. The subdomains may be separated by other sequences on the amino acid sequence of the protein. [075] Examples of REC domains include any polypeptides having a structural similarity and/or sequence similarity to a REC domain described in the art. For example, the REC domain may share a structural similarity and/or sequence similarity to a REC of Cas12a. In some examples, the REC domain may have an amino acid sequence that share at least 80%, at least 85%, at least 90%, at least 95%, at least 99%, or 100% sequence identity with REC domains. [076] In some examples, the REC domain comprise REC1 polypeptide and REC2 polypeptide. Examples of the REC1 domain also include any polypeptides having a structural similarity and/or sequence similarity to a REC1 and REC2 domains described in the art, such as the corresponding domains of Cas12a. The REC domain may have an amino acid sequence that share at least 80%, at least 85%, at least 90%, at least 95%, at least 99%, or 100% sequence identity with a REC domain of Cas12a. [077] The REC domain of Cas12a consists of the REC1 and REC2 domains where REC1 comprises 13 alpha helices, and REC2 comprises ten alpha helices and two beta strands that form a small antiparallel sheet (see e.g., Yamano et al.(2016) Cell, 165(4) pp.949-962). WED Domain [078] The Wedge (WED) domain may comprise multiple subdomains: WED-I, WED-II, and WED- III. The subdomains may be separated by other sequences on the amino acid sequence of the protein. [079] Examples of WED domains include any polypeptides having a structural similarity and/or sequence similarity to a WED domain described in the art. For example, the WED domain may share a structural similarity and/or sequence similarity to a WED of Cas12a. In some examples, the WED 15

domain may have an amino acid sequence that share at least 80%, at least 85%, at least 90%, at least 95%, at least 99%, or 100% sequence identity with WED domains. [080] In some examples, the WED domain comprise WED-I polypeptide, a WED-II polypeptide, and a WED-III polypeptide. Examples of the WED-I domain also include any polypeptides having a structural similarity and/or sequence similarity to a WED-I, WED-II, and WED-III domains described in the art, such as the corresponding domains of Cas12a. The WED domain may have an amino acid sequence that share at least 80%, at least 85%, at least 90%, at least 95%, at least 99%, or 100% sequence identity with a WED domain of Cas12a. [081] The WED domain of Cas12a is assembled from three separate regions (WED-I-III). The WED domain can be divided into a core subdomain comprising a nine-stranded, distorted antiparallel β sheet flanked by seven α helices and a subdomain comprising two β strands and two α helices (see e.g., Yamano et al.(2016) Cell, 165(4) pp.949-962). PI Domain [082] The nucleic-acid guided nuclease comprises a PAM Interacting (PI) domain. In an embodiment, at least one domain shares a substantial structural similarity or sequence similarity to a PI domain described in the art. [083] Examples of PI domains include any polypeptides having a structural similarity and/or sequence similarity to a PI domain described in the art. For example, the PI domain may share a structural similarity and/or sequence similarity to a PI of Cas12a. In some examples, the PI domain may have an amino acid sequence that share at least 80%, at least 85%, at least 90%, at least 95%, at least 99%, or 100% sequence identity with PI domains. [084] The PI domain of Cas12a is domain comprises seven α helices and a β hairpin and is inserted between the WED-II and WED-III regions (see e.g., Yamano et al.(2016) Cell, 165(4) pp.949-962). Modified RGN peptides [085] The RGNs may comprise one or more modifications. The modified RGNs may be catalytically inactive (also referred as dead). A catalytically inactive or dead nuclease may have reduced or no nuclease activity compared to a wildtype counterpart nuclease. In some cases, a catalytically inactive or dead nuclease may not have nickase activity. Such a catalytically inactive or dead RGN may not make either double-strand or single-strand break on a target polynucleotide but may still bind or otherwise form complex with the target polynucleotide. In an embodiment, the RGN polypeptide comprises a mutation of the catalytic RuvC- residue corresponding to D956A, E1050A or D1291A (catalytic residues of RuvI, II, and III) of SEQ ID NO: 371 (dEGS0081) or equivalent residues of other RGN sequences provided herein (see for example Kleinstiver, et al. (2019) Nat Biotechnol 37, 276–282). [086] In some embodiments, the RGN polypeptide comprises mutations in the DNA binding pocket to increase affinity for DNA leading to enhanced binding activity. Such enhanced binding activity can 16

lead to increased cleavage activity or can lead to increased activity of the fusion domain. In an embodiment, the RGN polypeptide comprises a mutation of Q167R, N575R, and/or K581R of SEQ ID NO: 372 (mutated EGS0068) or equivalent residues of other RGN sequences provided herein (see for example Kleinstiver, et al. (2019) Nat Biotechnol 37, 276–282). [087] In one embodiment, the modifications of the RGN polypeptide may or may not cause an altered functionality. Some modifications will not result in an altered functionality include for instance codon optimization for expression into a particular host or providing the nuclease with a particular marker. Modifications which may result in altered functionality may also include mutations, including point mutations, insertions, deletions, truncations (including split nucleases), etc., as well as chimeric RGNs (e.g., comprising domains from different orthologues or homologues) or fusion proteins. [088] Fusion proteins may include, for example, fusions with heterologous domains or functional domains (e.g., localization signals, enzymes). In an embodiment, various different modifications may be combined (e.g., a mutated nuclease which is catalytically inactive and which further is fused to a functional domain, such as for instance to induce DNA methylation or another nucleic acid modification, such as, for example, a mutation, a deletion, an insertion, a replacement. Localization signal sequences [089] The RGNs can comprise at least one nuclear localization signal (NLS) to enhance transport of the RGN to the nucleus of a cell. Nuclear localization signals are known in the art and generally comprise a stretch of basic amino acids (see, e.g., Lange et al., J. Biol. Chem. (2007) 282:5101-5105). In embodiments, the RGN comprises 2, 3, or more nuclear localization signals. The nuclear localization signal(s) can be a heterologous NLS. Non-limiting examples of nuclear localization signals useful for the presently disclosed RGNs are the nuclear localization signals of SV40 Large T- antigen, nucleopasmin, and c-Myc (see. e.g., Ray et al. (2015) Bioconjug Chem 26(6): 1004-7). In particular embodiments, the RGN comprises the NLS sequence comprising the sequence of SEQ ID NO: 111 and/or SEQ ID NO: 112. The RGN may comprise one or more NLS sequences at its N- terminus, C- terminus, or both the N-terminus and C- terminus. For example, the RGN may comprise two NLS sequences at the N-terminal region and four NLS sequences at the C-terminal region. [090] Other localization signal sequences known in the art that localize polypeptides to particular subcellular location(s) can also be used to target the RGNs, including, but not limited to, plastid localization sequences, mitochondrial localization sequences, and dual-targeting signal sequences that target to both the plastid and mitochondria (see, e.g., Nassoury and Morse (2005) Biochim Biophys Acta 1743:5-19; Herrmann and Neupert (2003) IUBMB Life 55:219-225; Soil (2002) Curr Opin Plant Biol 5:529-535; Carrie and Small (2013) Biochim Biophys Acta 1833:253-259). [091] In certain embodiments, the RGNs comprise at least one cell- penetrating domain that facilitates cellular uptake of the RGN. Cell-penetrating domains are known in the art and generally comprise 17

stretches of positively charged amino acid residues (i.e., polycationic cell- penetrating domains), alternating polar amino acid residues and non-polar amino acid residues (i.e., amphipathic cell- penetrating domains), or hydrophobic amino acid residues (i.e., hydrophobic cell- penetrating domains) (see, e.g., Milletti F. (2012) Drug Discov Today 17:850-860). A non-limiting example of a cell-penetrating domain is the trans-activating transcriptional activator (TAT) from the human immunodeficiency virus 1. [092] The nuclear localization signal, plastid localization signal, mitochondrial localization signal, dual targeting localization signal, and/or cell-penetrating domain can be located at the amino-terminus (N- terminus), the carboxyl-terminus (C-terminus), or in an internal location of the RNA-guided nuclease. Additional tags and labels [093] The presently disclosed RGN polypeptides can comprise a detectable label or a purification tag. The detectable label or purification tag can be located at the N-terminus, the C-terminus, or an internal location of the RNA-guided nuclease, either directly or indirectly via a linker peptide. In some of these embodiments, the RGN component of the fusion protein is a nuclease-dead RGN. In other embodiments, the RGN component of the fusion protein is a RGN with nickase activity. [094] RGNs that lack nuclease activity can be used to deliver a fused polypeptide, polynucleotide, or small molecule payload to a particular genomic location. In some of these embodiments, the RGN polypeptide or guide RNA can be fused to a detectable label to allow for detection of a particular sequence. As a non-limiting example, a nuclease-dead RGN can be fused to a detectable label (e.g., fluorescent protein) and targeted to a particular sequence associated with a disease to allow for detection of the disease-associated sequence. [095] A detectable label is a molecule that can be visualized or otherwise observed. The detectable label may be fused to the RGN as a fusion protein (e.g., fluorescent protein) or may be a small molecule conjugated to the RGN polypeptide that can be detected visually or by other means. Detectable labels that can be fused to the presently disclosed RGNs as a fusion protein include any detectable protein domain, including but not limited to, a fluorescent protein or a protein domain that can be detected with a specific antibody. Non-limiting examples of fluorescent proteins include green fluorescent proteins (e.g., GFP, EGFP, ZsGreenl) and yellow fluorescent proteins (e.g., YFP, EYFP, ZsYellowl). Non-limiting examples of small molecule detectable labels include radioactive labels, such as ³H and ³⁵S. [096] RGN polypeptides can also comprise a purification tag, which is any molecule that can be utilized to isolate a protein or fused protein from a mixture (e.g., biological sample, culture medium). Non-limiting examples of purification tags include biotin, myc, maltose binding protein (MBP), and glutathione -S- transferase (GST). 18

Fusion proteins comprising the RGNs [097] The presently disclosed RGNs can be fused to an effector domain (a fusion protein of an RGN and an effector domain) , such as a cleavage domain, a deaminase domain, or an expression modulator domain, either directly or indirectly via a linker. Such effector domain can be located at the N- terminus, the C-terminus, or an internal location of the RNA-guided nuclease. In some embodiments, the RGN component of the fusion protein is a nuclease-dead RGN. [098] RGNs that are fused to a polypeptide or domain can be separated or joined by a linker. In some embodiments, a linker joins a crRNA binding domain of an RNA guided nuclease and a base-editing polypeptide, such as a deaminase. [099] In some embodiments, the RGN fusion protein comprises a cleavage domain, which is any domain that is capable of cleaving a polynucleotide (i.e., RNA, DNA) and includes, but is not limited to, restriction endonucleases and homing endonucleases (see, e.g., Linn et al. (eds.) Nucleases, Cold Spring Harbor Laboratory Press, 1993). [100] In some embodiments, the RGN fusion protein comprises a deaminase domain that deaminates a nucleotide base, resulting in conversion from one nucleotide base to another, and includes, but is not limited to, a cytidine deaminase or an adenosine deaminase base editor. [101] In some embodiments, the effector domain of the fusion protein can be an expression modulator domain, which is a domain that either serves to upregulate or downregulate transcription. The expression modulator domain can be an epigenetic modification domain, a transcriptional repressor domain or a transcriptional activation domain. [102] In some of these embodiments, the expression modulator of the RGN fusion protein comprises an epigenetic modification domain that covalently modifies DNA or histone proteins to alter histone structure and/or chromosomal structure without altering the DNA sequence, leading to changes in gene expression (i. e., upregulation or downregulation). Non-limiting examples of epigenetic modifications include acetylation or methylation of lysine residues, arginine methylation, serine and threonine phosphorylation, and lysine ubiquitination and sumoylation of histone proteins, and methylation and hydroxymethylation of cytosine residues in DNA. Non-limiting examples of epigenetic modification domains include histone acetyltransferase domains, histone deacetylase domains, histone methyltransferase domains, histone demethylase domains, DNA methyltransferase domains, and DNA demethylase domains. [103] In other embodiments, the expression modulator of the fusion protein comprises a transcriptional repressor domain, which interacts with transcriptional control elements and/or transcriptional regulatory proteins, such as RNA polymerases and transcription factors, to reduce or 19

terminate transcription of at least one gene. Transcriptional repressor domains are known in the art and include, but are not limited to IKB, and Kruppel associated box (KRAB) domains. [104] In yet other embodiments, the expression modulator of the fusion protein comprises a transcriptional activation domain, which interacts with transcriptional control elements and/or transcriptional regulatory proteins, such as RNA polymerases and transcription factors, to increase or activate transcription of at least one gene. Transcriptional activation domains are known in the art and include, but are not limited to, a VP16 activation domain and an NFAT activation domain. [105] It is also envisaged that the nucleic acid-targeting effector protein-guide RNA complex as a whole may be associated with two or more functional domains. For example, there may be two or more functional domains associated with the nucleic acid-targeting effector protein, or there may be two or more functional domains associated with the guide RNA (via one or more adaptor proteins), or there may be one or more functional domains associated with the nucleic acid-targeting effector protein and one or more functional domains associated with the guide RNA (via one or more adaptor proteins). [106] The fusion between the adaptor protein and the activator or repressor may include a linker. For example, GlySer linkers GGGS can be used. They can be used in repeats of 3 or 6, 9 or even 12 or more, to provide suitable lengths, as required. Linkers can be used between the guide RNAs and the functional domain (activator or repressor), or between the nucleic acid-targeting effector protein and the functional domain (activator or repressor). CRISPR repeats RNAs and crRNA [107] The present disclosure provides RGNs that can bind to CRISPR repeat RNAs or crRNAs. A crRNA is one RNA molecule, that can bind to the RGN and guide the RGN to bind to a particular target nucleotide sequence, and in those instances wherein the RGN has nuclease activity, also cleave the target nucleotide sequence. [108] A crRNA comprises a spacer sequence and a CRISPR repeat sequence. In the context of the present disclosure, a crRNA comprises a repeat sequence, or a partial CRISPR repeat sequence. Native direct repeat sequences within a CRISPR array generally range in length from 28 to 37 base pairs, although the length can vary between about 23 bp to about 55 bp. Spacer sequences within a CRISPR array generally range from about 32 to about 38 bp in length, although the length can be between about 21 bp to about 72 bp. Each CRISPR array generally comprises less than 50 units of the CRISPR repeat-spacer sequence. The CRISPRs are transcribed as part of a long transcript termed the primary CRISPR transcript, which comprises much of the CRISPR array. The primary CRISPR transcript is cleaved by Cas proteins to produce crRNAs or in some cases, to produce pre-crRNAs that are further processed by additional Cas proteins into mature crRNAs. Type V-A systems are capable of self-processing the primary CRISPR transcript, unlike Cas9 systems which rely on other proteins to 20

process the transcript. Mature crRNAs comprise a CRISPR repeat sequence (or a part thereof) and a spacer sequence. In some embodiments in which pre-crRNAs are processed into mature (or processed) crRNAs, maturation involves the removal of 1 to 6 or more 5', 3', or 5' and 3' nucleotides. For the purposes of genome editing or targeting a particular target nucleotide sequence of interest, these nucleotides that are removed during maturation of the pre-crRNA molecule are not necessary for generating or designing a crRNA. [109] In the context of the present disclosure, the part of the CRIPSR repeat sequence present in crRNA forms a stem-loop structure. This stem-loop structure is typically in the range of 15 to 22 nucleotides in length. Substitutions that disrupt this stem-loop duplex abolish cleavage activity, whereas other substitutions that do not disrupt the stem-loop duplex do not abolish cleavage activity. The crRNA forms a stem-loop structure at the 5 ' end, and the sequence at the 3' end is a spacer sequence complementary to a sequence in a target nucleic acid sequence. [110] The spacer sequence is engineered to be fully or partially complementary with the target sequence of interest. In various embodiments, the spacer sequence can comprise from about 8 nucleotides to about 30 nucleotides, or more. For example, the spacer sequence can be 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more nucleotides in length. In some embodiments, the spacer sequence is 10 to 26 nucleotides in length, or 12 to 30 nucleotides in length. In particular embodiments, the spacer sequence is 20-23 nucleotides in length. [111] More specifically, in the crRNA, the length of the spacer sequence is 17 to 23bp, 18 to 23bp, 19 to 23bp, more specifically 20 to 23bp, as more specifically, it may be a 21 to 23bp, but is not limited thereto. [112] Specific sequences corresponding to the RGN polypeptides of the present disclosure are provided in Table5. The crRNA RGN-interacting sequence is a sequence obtained from the consensus repeat CRISPR sequence. The crRNA sequences are example sequences containing both crRNA RGN-interacting sequence and a spacer sequence of 23 nt. [113] Table 5. RGN CRISPR repeat and crRNA sequences

21

[114] The crRNA can be synthesized chemically or via in vitro transcription. Assays for determining sequence-specific binding between a RGN and a crRNA are known in the art and include, but are not limited to, in vitro binding assays between an expressed RGN and the crRNA, which can be tagged with a detectable label and used in a pull-down detection assay in which the crRNA:RGN complex is captured via the detectable label (e.g., with streptavidin beads). A control crRNA with an unrelated sequence or structure to the crRNA can be used as a negative control for non-specific binding of the RGN to RNA. [115] In certain embodiments, the crRNA can be introduced into a target cell, organelle, or embryo as an RNA molecule. The crRNA can be transcribed in vitro or chemically synthesized. In other embodiments, a nucleotide sequence encoding the crRNA is introduced into the cell, organelle, or embryo. In some of these embodiments, the nucleotide sequence encoding the crRNA is operably linked to a promoter (e.g. , an RNA polymerase III promoter). The promoter can be a native promoter or heterologous to the crRNA-encoding nucleotide sequence. 22

[116] In various embodiments, the crRNA can be introduced into a target cell, organelle, or embryo as a ribonucleoprotein complex, as described herein, wherein the crRNA is bound to an RNA-guided nuclease polypeptide. The crRNA directs an associated RNA-guided nuclease to a particular target nucleotide sequence of interest through hybridization of the crRNA to the target nucleotide sequence. A target nucleotide sequence can comprise DNA, RNA, or a combination of both and can be single- stranded or double -stranded. A target nucleotide sequence can be genomic DNA (i.e. , chromosomal DNA), plasmid DNA, or an RNA molecule ( e.g . , messenger RNA, ribosomal RNA, transfer RNA, micro RNA, small interfering RNA). The target nucleotide sequence can be bound (and in some embodiments, cleaved) by an RNA-guided nuclease in vitro or in a cell. The chromosomal sequence targeted by the RGN can be a nuclear, plastid or mitochondrial chromosomal sequence. In some embodiments, the target nucleotide sequence is unique in the target genome. Multiple crRNA molecules [117] The present disclosure also provides methods for binding and/or modifying a target nucleotide sequence of interest. The methods include delivering a system comprising at least one crRNA or a polynucleotide encoding the same, and at least one fusion polypeptide comprises an RGN of the invention and a base-editing polypeptide, for example a cytidine deaminase or an adenosine deaminase, or a polynucleotide encoding the fusion polypeptide, to the target sequence or a cell, organelle, or embryo comprising the target sequence. [118] One of ordinary skill in the art will appreciate that any of the presently disclosed methods can be used to target a single target sequence or multiple target sequences. Thus, methods comprise the use of a single RGN polypeptide in combination with multiple, distinct crRNAs, which can target multiple, distinct sequences within a single gene and/or multiple genes. Also encompassed herein are methods wherein multiple, distinct crRNAs are introduced in combination with multiple, distinct RGN polypeptides. These crRNAs and crRNA/RGN polypeptide systems can target multiple, distinct sequences within a single gene and/or multiple genes. Protospacer adjacent motif (PAM) sequences [119] In the context of the RGNs disclosed herein, the target nucleotide sequence of the RGNs is adjacent to a sequence called protospacer adjacent motif (PAM). A protospacer adjacent motif is generally within about 1 to about 30 nucleotides from the target nucleotide sequence. A protospacer adjacent motif is can be within 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides from the target nucleotide sequence. The PAM can be 5' or 3' of the target sequence depending on the RGN. In some embodiments, the PAM is 5' of the target sequence for the presently disclosed RGNs. Generally, the PAM is a consensus sequence of about 3-4 nucleotides, but in particular embodiments, can be 2, 3, 4, 5, 6, 7, 8, 9, or more nucleotides in length. [120] Table 6. PAM sequences for the RGNs 23

[121] In particular embodiments, an RGN listed in the table above or an active variant or fragment thereof binds respectively a target nucleotide sequence adjacent to a respective PAM sequence set forth in Table 6. [122] It is well-known in the art that PAM sequence specificity for a given nuclease enzyme is affected by enzyme concentration (see, e.g. , Karvelis et al. (2015) Genome Biol 16:253), which may be modified by altering the promoter used to express the RGN, or the amount of ribonucleoprotein complex delivered to the cell, organelle, or embryo. [123] Upon recognizing its corresponding PAM sequence, the RGN can cleave the target nucleotide sequence at a specific cleavage site. As used herein, a cleavage site is made up of the two particular nucleotides within a target nucleotide sequence between which the nucleotide sequence is cleaved by an RGN. The cleavage site can comprise the 1st and 2nd, 2nd and 3rd, 3rd and 4th, 4th and 5th, 5th and 6th, 7th and 8th, or 8th and 9th nucleotides from the PAM in either the 5' or 3' direction. In some embodiments, the cleavage site may be over 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides 24

from the PAM in either the 5’ or 3’ direction. In some embodiments, the cleavage site is 4 nucleotides away from the PAM. In other embodiments, the cleavage site is at least 15 nucleotides away from the PAM. As RGNs can cleave a target nucleotide sequence resulting in staggered ends, in some embodiments, the cleavage site is defined based on the distance of the two nucleotides from the PAM on the positive (+) strand of the polynucleotide and the distance of the two nucleotides from the PAM on the negative (-) strand of the polynucleotide. Target nucleotide sequence [124] The target polynucleotide of an RGN system can be any polynucleotide endogenous or exogenous to a procaryotic or eukaryotic cell. For example, the target polynucleotide can be a polynucleotide residing in the nucleus of the eukaryotic cell. The target polynucleotide can be a sequence coding a gene product (e.g., a protein) or a non-coding sequence (e.g., an intron). The target sequence is generally associated with a PAM (protospacer adjacent motif). The precise sequence and length requirements for the PAM differ depending on the RGN used, but PAMs are typically 2-5 base pair sequences adjacent the target sequence. [125] The target polynucleotide of an RGN/RNA complex may be a disease-associated gene or polynucleotides or a gene/ polynucleotide associated with a biological pathway. RGNs complexes with RNA [126] RGNs proteins can be complexed to an RNA (RNA/RGN complex) in order to deliver RGN in proximity with a target nucleic acid sequence. The RNA, such as a crRNA, is a polynucleotide that site-specifically guides an RGN, or a deactivated RGN, to a target nucleic acid region. The binding specificity is determined jointly by the complementary region on the cognate guide and a short DNA motif (protospacer adjacent motif or PAM) juxtaposed to the complementary region. The spacer present in the crRNA specifically hybridizes to a target nucleic acid sequence and determines the location of a RGN protein's site-specific binding and nucleolytic cleavage. [127] RNA/RGN complexes can be produced using methods well known in the art. For example, the RNA of the complexes can be produced in vitro and RGN polypeptides can be recombinantly produced and then the RNA and RGN proteins can be complexed together using methods known in the art. Additionally, cell lines constitutively expressing RGN proteins can be developed and can be transfected with the crRNA components, and complexes can be purified from the cells using standard purification techniques, such as but not limited to affinity, ion exchange and size exclusion chromatography. See, e.g., Jinek M., et al, "A programmable dual-R A-guided DNA endonuclease in adaptive bacterial immunity," Science (2012) 337:816-821. [128] Alternatively, the components, i.e., the crRNA and RGN polynucleotides may be provided separately to a cell, e.g., using separate constructs, or together, in a single construct, or in any combination, and complexes can be purified as above. 25

[129] Methods of designing particular crRNA, such as for use in the complexes, are known. See, e.g., Briner et al., "Guide RNA Functional Modules Direct Cas9 Activity and Orthogonality," Molecular Cell (2014) 56:333-339. To do so, the genomic sequence for the gene to be targeted is first identified. The exact region of the selected gene to target will depend on the specific application. For example, in order to activate or repress a target gene using, for example, Cas activators or repressors, crRNA/RGN complexes can be targeted to the promoter driving expression of the gene of interest. For genetic knockouts, crRNAs are commonly designed to target 5' constitutively expressed exons which reduces the chances or removal of the targeted region from mRNA due to alternative splicing. Exons near the N- terminus can be targeted because frameshift mutations here will increase the likelihood of the production of a nonfunctional protein product. Alternatively, cognate crRNAs can be designed to target exons that code for known essential protein domains. In this regard, non-frameshift mutations such as insertions or deletions are more likely to alter protein function when they occur in protein domains that are essential for protein function. For gene editing using HDR, the target sequence should be close to the location of the desired edit. In this case, the location where the edit is desired is identified and a target sequence is selected nearby. [130] The crRNA can be delivered to a cell. If the cell constitutively expresses a RGN, the RGN will then be recruited to the target site to cleave the target nucleic acid. If the cell does not express an RGN, complexes of crRNA/RGN can be delivered to the cells to make breaks in the genome, thereby triggering the repair pathways in the cells. [131] Treated cells are then screened using methods well known in the art, such as using high- throughput screening techniques including, but not limited to, fluorescence-activated cell sorting (FACS)-based screening platforms, microfluidics-based screening platforms, and the like. These techniques are well known in the art. See, e.g., Wojcik et al, Int. J. Molec. Sci. (2015) 16:24918- 24945. The cells can then be expanded and re-transfected with additional RGN/gRNA complexes to introduce further diversity and this process can be repeated iteratively until a population with the desired properties is obtained. Single cell clones are sorted from the population, expanded and sequenced to recover the mutations that resulted in the desired function. Variants of the RGNs [132] The present disclosure provides RGNs comprising at least 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100 or more contiguous amino acid residues of an amino acid sequence set forth in Table 4. RNA-guided nucleases provided herein can comprise at least one nuclease domain (e.g ., DNase, RNase domain) and at least one RNA recognition and/or RNA binding domain to interact with crRNAs. Further domains that can be found in RNA-guided nucleases provided herein include, but are not limited to, DNA binding domains, helicase domains, protein-protein interaction domains, and dimerization domains. In specific embodiments, the RNA-guided nucleases provided herein can comprise at least 70%, 75%, 80%, 26

85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% to one or more of a DNA binding domains, helicase domains, protein-protein interaction domains, and dimerization domains. [133] While the activity of a variant or fragment may be altered compared to the polynucleotide or polypeptide of interest, the variant and fragment should retain the functionality of the polynucleotide or polypeptide of interest. For example, a variant or fragment may have increased activity, decreased activity, different spectrum of activity or any other alteration in activity when compared to the polynucleotide or polypeptide of interest. [134] Fragments and variants of naturally-occurring RGN polypeptides, such as those disclosed herein, will retain sequence-specific, RNA-guided DNA-binding activity. In particular embodiments, fragments and variants of naturally-occurring RGN polypeptides, such as those disclosed herein, will retain nuclease activity (single -stranded or double-stranded). [135] A biologically active variant of an RGN polypeptide of the invention may differ by as few as about 1-15 amino acid residues, as few as about 1-10, such as about 6-10, as few as 5, as few as 4, as few as 3, as few as 2, or as few as 1 amino acid residue. In specific embodiments, the polypeptides can comprise an N- terminal or a C-terminal truncation, which can comprise at least a deletion of 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050 amino acids or more from either the N or C terminus of the polypeptide. Variants of crRNA [136] RGN proteins can have varying sensitivity to mismatches between a spacer sequence in a crRNA and its target sequence that affects the efficiency of cleavage. The CRISPR RNA repeat sequence comprises a nucleotide sequence that comprises a region with sufficient complementarity to form a mature crRNA. In various embodiments, the CRISPR RNA repeat sequence can comprise from about 8 nucleotides to about 30 nucleotides, or more. For example, the CRISPR repeat sequence can be about 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more nucleotides in length. In some embodiments, the CRISPR repeat sequence is 20-22 nucleotides in length. In particular embodiments, the CRISPR repeat sequence comprises the nucleotide sequence set forth in Table 5, or an active variant or fragment thereof that when comprised within a crRNA, is capable of directing the sequence-specific binding of an associated RNA-guided nuclease provided herein to a target sequence of interest. In certain embodiments, an active CRISPR repeat sequence variant of a wild-type sequence comprises a nucleotide sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the CRISPR repeat nucleotide sequence set forth in Table 5. In certain embodiments, an active CRISPR repeat sequence fragment of a wild-type sequence comprises at least 27

5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 contiguous nucleotides of the CRISPR repeat nucleotide sequence set forth in Table 5. [137] Fragments and variants of naturally-occurring CRISPR repeats, such as those disclosed herein, will retain the ability, when part of a crRNA), to bind to and guide an RNA-guided nuclease (complexed with the crRNA) to a target nucleotide sequence in a sequence-specific manner. [138] It will be appreciated that crRNA RGN-interacting sequences of most of the RGN polypeptides of the present disclosure are very similar in the sequence and could be modified, provided such sequences maintain stem-loop structure that is important for their interaction with an RGN. [139] Fragments and variants of naturally-occurring crRNAs, such as those disclosed herein, will retain the ability, to guide an RNA-guided nuclease to a target nucleotide sequence in a sequence- specific manner. [140] In various embodiments, the hairpin forming region of the crRNA that is produced from the CRISPR repeat sequence comprises from about 8 nucleotides to about 30 nucleotides, or more. For example, the region of the CRISPR repeat sequence can be 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more nucleotides in length. [141] In certain embodiments, the presently disclosed polynucleotides comprise or encode a CRISPR repeat comprising a nucleotide sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater identity to the CRISPR repeat nucleotide sequence set forth in Table 5. [142] The presently disclosed polynucleotides can comprise or encode a part of the crRNA interacting with the RGN comprising a nucleotide sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater identity to the crRNA RGN-interacting nucleotide sequence set forth in Table 5. [143] Biologically active variants of a CRISPR repeat part of the disclosure present in crRNA may differ by as few as about 1-15 nucleotides, as few as about 1-10, such as about 6-10, as few as 5, as few as 4, as few as 3, as few as 2, or as few as 1 nucleotides. In specific embodiments, the polynucleotides can comprise a 5' or 3' truncation, which can comprise at least a deletion of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 nucleotides or more from either the 5' or 3' end of the polynucleotide. Variants of spacer sequences [144] In some embodiments, the degree of complementarity between a spacer sequence and its corresponding target sequence, when optimally aligned using a suitable alignment algorithm, is about or more than 80%, 85%, 90, 95%, 96%, 97%, 98%, 99%, or more. In particular embodiments, the 28

spacer sequence is free of secondary structure, which can be predicted using any suitable polynucleotide folding algorithm known in the art, including but not limited to mFold (see, e.g., Zuker and Stiegler (1981) Nucleic Acids Res .9: 133-148) and RNAfold (see, e.g., Gruber et al. (2008) Cell l06(l):23-24). Nucleotides encoding RNA-guided nucleases and/or crRNA [145] The present disclosure provides polynucleotides comprising the presently disclosed CRISPR RNAs, and/or crRNAs and polynucleotides comprising a nucleotide sequence encoding the presently disclosed RNA-guided nucleases, CRISPR RNAs, and/or crRNAs. Presently disclosed polynucleotides include those comprising or encoding a CRISPR repeat sequence comprising the nucleotide sequence set forth in Table 5, or an active variant or fragment thereof that when comprised within a crRNA is capable of directing the sequence-specific binding of an associated RNA- guided nuclease to a target sequence of interest. [146] The disclosure also provides polynucleotides comprising or encoding a crRNA comprising the nucleotide sequence set forth in Table 5, or an active variant or fragment thereof that is capable of directing the sequence- specific binding of an associated RNA-guided nuclease to a target sequence of interest. Polynucleotides are also provided that encode an RNA-guided nuclease comprising the amino acid sequence set forth in Table 4, and active fragments or variants thereof that retain the ability to bind to a target nucleotide sequence in an RNA-guided sequence-specific manner. [147] The expression cassette will include in the 5'-3' direction of transcription, a transcriptional (and, in some embodiments, translational) initiation region (i.e.. a promoter), an RGN-, a transcriptional initiation region (i.e.. a promoter), crRNA, encoding polynucleotide, and a transcriptional (and in some embodiments, translational) termination region (i.e.. termination region) functional in the organism of interest. The promoters of the invention are capable of directing or driving expression of a coding sequence in a host cell. The regulatory regions (e.g., promoters, transcriptional regulatory regions, and translational termination regions) may be endogenous or heterologous to the host cell or to each other. [148] Additional regulatory signals may include, but are not limited to, transcriptional initiation start sites, operators, activators, enhancers, other regulatory elements, ribosomal binding sites, an initiation codon, and termination signals. [149] In preparing the expression cassette, the various DNA fragments may be manipulated, so as to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame. Toward this end, adapters or linkers may be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like. For this purpose, in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions, may be involved. 29

[150] A number of promoters can be used in the practice of the invention. The promoters can be selected based on the desired outcome. The nucleic acids can be combined with constitutive, inducible, growth stage-specific, cell type-specific, tissue-preferred, tissue-specific, or other promoters for expression in the organism of interest. [151] In some embodiments, the nucleotide comprises a tissue-preferred promoter. In some embodiments, the nucleic acid molecules encoding a RGN and/or crRNA comprise a cell type- specific promoter. [152] The nucleic acid sequences encoding the RGNs and/or crRNA can be operably linked to a promoter sequence that is recognized by a phage RNA polymerase for example, for in vitro mRNA synthesis. For example, the promoter sequence can be a pol I, pol II, pol III, T7, T3, U6, CMV or SP6 promoter sequence or a variation of a T7, T3, U6, CMV or SP6 promoter sequence. In such embodiments, the expressed protein and/or RNAs can be purified for use in the methods of genome modification described herein. Any Pol II promoter or terminator could express the RGN. The choice of a promoter depends on how strongly RGN needs to be expressed and in what tissue type. In a preferred embodiment the RGN is expressed using is the CMV promoter. The crRNA can be expressed by Pol III promoters (e.g. U6 promoter). [153] In certain embodiments, the polynucleotide encoding the RGN also can be linked to a polyadenylation signal (e.g., SV40 polyA signal, or sv40 polyA with rrnG terminator) and/or at least one transcriptional termination sequence. Additionally, the sequence encoding the RGN also can be linked to sequence(s) encoding at least one nuclear localization signal, at least one cell- penetrating domain, and/or at least one signal peptide capable of trafficking proteins to particular subcellular locations. [154] Additional regulatory signals include, but are not limited to, transcriptional initiation start sites, operators, activators, enhancers, other regulatory elements, ribosomal binding sites, an initiation codon, termination signals, and the like. See, for example, U.S. Pat. Nos.5,039,523 and 4,853,331 [155] In preparing the expression cassette, the various DNA fragments may be manipulated, so as to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame. Toward this end, adapters or linkers may be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like. For this purpose, in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions, may be involved. Variants of polynucleotides [156] For polynucleotides, conservative variants include those sequences that, because of the degeneracy of the genetic code, encode the native amino acid sequence of the gene of interest. 30

Naturally occurring allelic variants such as these can be identified with the use of well-known molecular biology techniques, as, for example, with polymerase chain reaction (PCR) and hybridization techniques as outlined below. Variant polynucleotides also include synthetically derived polynucleotides, such as those generated, for example, by using site-directed mutagenesis but which still encode the polypeptide or the polynucleotide of interest. Generally, variants of a particular polynucleotide disclosed herein will have at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to that particular polynucleotide as determined by sequence alignment programs and parameters described elsewhere herein. [157] Variants of a particular polynucleotide disclosed herein (i.e. , the reference polynucleotide) can also be evaluated by comparison of the percent sequence identity between the polypeptide encoded by a variant polynucleotide and the polypeptide encoded by the reference polynucleotide. Percent sequence identity between any two polypeptides can be calculated using sequence alignment programs and parameters described elsewhere herein. Where any given pair of polynucleotides disclosed herein is evaluated by comparison of the percent sequence identity shared by the two polypeptides they encode, the percent sequence identity between the two encoded polypeptides is at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity. [158] In particular embodiments, the presently disclosed polynucleotides encode an RGN polypeptide comprising an amino acid sequence having at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater identity to an amino acid sequence set forth in Table 4. [159] Variant polynucleotides and proteins also encompass sequences and proteins derived from a mutagenic and recombinogenic procedure such as DNA shuffling. With such a procedure, one or more different RGN proteins disclosed herein is manipulated to create a new RGN protein possessing the desired properties. In this manner, libraries of recombinant polynucleotides are generated from a population of related sequence polynucleotides comprising sequence regions that have substantial sequence identity and can be homologously recombined in vitro or in vivo. For example, using this approach, sequence motifs encoding a domain of interest may be shuffled between the RGN sequences provided herein and other known RGN genes to obtain a new gene coding for a protein with an improved property of interest, such as an increased Km in the case of an enzyme. Strategies for such DNA shuffling are known in the art. See, for example, Stemmer (1994) Proc. Natl. Acad. Sci. USA Codon-optimized sequences 31

[160] The nucleic acid molecules encoding RNA-guided nucleases, and/or crRNAs can be codon optimized for expression in a target cell or tissue of interest. Such polynucleotide coding sequence normally has its frequency of codon usage designed to mimic the frequency of preferred codon usage or transcription conditions of a particular host cell. Expression in the particular host cell or organism is enhanced as a result of the alteration of one or more codons at the nucleic acid level such that the translated amino acid sequence is not changed. Nucleic acid molecules can be codon optimized, either wholly or in part. Codon tables and other references providing preference information for a wide range of organisms are available in the art. Vectors [161] The polynucleotide encoding the RGN and/or crRNA can be present in a vector or multiple vectors. Suitable vectors include plasmid vectors, phagemids, cosmids, artificial/mini-chromosomes, transposons, and viral vectors (e.g., lentiviral vectors, adeno-associated viral vectors, baculoviral vector). The vector can comprise additional expression control sequences (e.g., enhancer sequences, Kozak sequences, polyadenylation sequences, transcriptional termination sequences), selectable marker sequences (e.g., antibiotic resistance genes), origins of replication, and the like. Additional information can be found in "Current Protocols in Molecular Biology" Ausubel et al, John Wiley & Sons, New York, 2003 or "Molecular Cloning: A Laboratory Manual" Sambrook & Russell, Cold Spring Harbor Press, Cold Spring Harbor, N.Y., 3rd edition, 2001. [162] The vector can also comprise a selectable marker gene for the selection of transformed cells. Selectable marker genes are utilized for the selection of transformed cells or tissues. Marker genes include genes encoding antibiotic resistance, such as those encoding neomycin phosphotransferase II (NEO) and hygromycin phosphotransferase (HPT), as well as genes conferring resistance to herbicidal compounds, such as glufosinate ammonium, bromoxynil, imidazolinones, and 2,4- dichlorophenoxyacetate (2,4-D). [163] In some embodiments, the expression cassette or vector comprising the sequence encoding the RGN polypeptide can further comprise a sequence encoding a crRNA. The sequence(s) encoding the crRNA can be operably linked to at least one transcriptional control sequence for expression of the crRNA in the organism or host cell of interest. For example, the polynucleotide encoding the crRNA can be operably linked to a promoter sequence that is recognized by RNA polymerase III (Pol III). Examples of suitable Pol III promoters include, but are not limited to, mammalian U6, U3, Hl, and 7SL RNA promoters and rice U6 and U3 promoters. Systems for binding to the target nucleotide sequence of interest [164] The present disclosure provides a system for binding a target sequence of interest, wherein the system comprises at least one crRNA or a nucleotide sequence encoding the same, and at least one RGN or a nucleotide sequence encoding the same. The crRNA hybridizes to the target sequence of 32

interest and also forms a complex with the RGN polypeptide, thereby directing the RGN polypeptide to bind to the target sequence. In some of these embodiments, the RGN comprises an amino acid sequence set forth in Table 4 or an active variant or fragment thereof. In various embodiments, the crRNA comprises a CRISPR repeat sequence comprising the nucleotide sequence set forth in Table 5 or an active variant or fragment thereof. In particular embodiments, the crRNA comprises a nucleotide sequence interacting with the RGN set forth in Table 5 or an active variant or fragment thereof. In particular embodiments, the system comprises a RGN that is heterologous to the crRNA, wherein the RGN and crRNA are not naturally complexed in nature. [165] The system for binding a target sequence of interest provided herein can be a ribonucleoprotein complex, which is at least one molecule of an RNA bound to at least one protein. The ribonucleoprotein complexes provided herein comprise at least one crRNA as the RNA component and an RNA-guided nuclease as the protein component. Such ribonucleoprotein complexes can be purified from a cell or organism that naturally expresses an RGN polypeptide and has been engineered to express a particular crRNA that is specific for a target sequence of interest. [166] Alternatively, the ribonucleoprotein complex can be purified from a cell or organism that has been transformed with polynucleotides that encode an RGN polypeptide and a crRNA and cultured under conditions to allow for the expression of the RGN polypeptide and crRNA. Thus, methods are provided for making an RGN polypeptide or an RGN ribonucleoprotein complex. Such methods comprise culturing a cell comprising a nucleotide sequence encoding an RGN polypeptide, and in some embodiments a nucleotide sequence encoding a crRNA, under conditions in which the RGN polypeptide (and in some embodiments, the crRNA) is expressed. The RGN polypeptide or RGN ribonucleoprotein can then be purified from a lysate of the cultured cells. [167] Methods for purifying an RGN polypeptide or RGN ribonucleoprotein complex from a lysate of a biological sample are known in the art (e.g., size exclusion and/or affinity chromatography, 2D- PAGE, HPLC, reversed-phase chromatography, immunoprecipitation). In particular methods, the RGN polypeptide is recombinantly produced and comprises a purification tag to aid in its purification, including but not limited to, glutathione-S-transferase (GST), chitin binding protein (CBP), maltose binding protein, thioredoxin (TRX), poly(NANP), tandem affinity purification (TAP) tag, myc, AcV5, AU1, AU5, E, ECS, E2, FLAG, HA, nus, Softag 1, Softag 3, Strep, SBP, Glu-Glu, HSV, KT3, S, Sl, T7, V5, VSV-G, 6xHis, lOxHis, biotin carboxyl carrier protein (BCCP), and calmodulin. [168] Generally, the tagged RGN polypeptide or RGN ribonucleoprotein complex is purified using immobilized metal affinity chromatography. It will be appreciated that other similar methods known in the art may be used, including other forms of chromatography or for example immunoprecipitation, either alone or in combination. 33

[169] Some methods provided herein for binding and/or cleaving a target sequence of interest involve the use of an in vitro assembled RGN ribonucleoprotein complex. In vitro assembly of an RGN ribonucleoprotein complex can be performed using any method known in the art in which an RGN polypeptide is contacted with a crRNA under conditions to allow for binding of the RGN polypeptide to the crRNA. The RGN polypeptide can be purified from a biological sample, cell lysate, or culture medium, produced via in vitro translation, or chemically synthesized. The crRNA can be purified from a biological sample, cell lysate, or culture medium, transcribed in vitro, or chemically synthesized. The RGN polypeptide and crRNA can be brought into contact in solution (e.g., buffered saline solution) to allow for in vitro assembly of the RGN ribonucleoprotein complex. Delivery of the components to the target cells [170] In some aspects, components of the present invention are delivered using nanoscale delivery systems, such as nanoparticles. Additionally, liposomes and other particulate delivery systems can be used. For example, vectors including the components of the present methods can be packaged in liposomes prior to delivery to the subject or to cells derived therefrom. Lipid encapsulation is generally accomplished using liposomes that are able to stably bind or entrap and retain nucleic acid. [171] As indicated, expression constructs comprising nucleotide sequences encoding the RGNs and/or crRNA can be used to transform organisms of interest. Methods for transformation involve introducing a nucleotide construct into an organism of interest. [172] The methods of the invention do not require a particular method for introducing a nucleotide construct to a host organism, only that the nucleotide construct gains access to the interior of at least one cell of the host organism. The host cell can be a eukaryotic or prokaryotic cell. In particular embodiments, the eukaryotic host cell is a plant cell, a mammalian cell, or an insect cell. Methods for introducing nucleotide constructs into plants and other host cells are known in the art including, but not limited to, stable transformation methods, transient transformation methods, and virus-mediated methods. [173] It is recognized that other exogenous or endogenous nucleic acid sequences or DNA fragments may also be incorporated into the host cell. Transformation of a host cell may be performed by infection, transfection, microinjection, electroporation, microprojection, biolistics or particle bombardment, electroporation, silica/carbon fibers, ultrasound mediated, PEG mediated, calcium phosphate co-precipitation, polycation DMSO technique, DEAE dextran procedure, and viral mediated, liposome mediated and the like. Viral -mediated introduction of a polynucleotide encoding an RGN and/or crRNA includes retroviral, lentiviral, adenoviral, and adeno-associated viral mediated introduction and expression, as well as the use of Caulimoviruses, Geminiviruses, and RNA plant viruses. [174] Transformation may result in stable or transient incorporation of the nucleic acid into the cell. 34

[175] The cells that have been transformed may be grown into a transgenic organism, such as a plant, in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84. These plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting hybrid having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure expression of the desired phenotypic characteristic has been achieved. In this manner, the present invention provides transformed seed (also referred to as "transgenic seed") having a nucleotide construct of the invention, for example, an expression cassette of the invention, stably incorporated into their genome. [176] Alternatively, cells that have been transformed may be introduced into an organism. These cells could have originated from the organism, wherein the cells are transformed in an ex vivo approach. [177] The polynucleotides encoding the RGNs or crRNAs can also be used to transform any prokaryotic species, including but not limited to, archaea and bacteria (e.g., Bacillus sp., Klebsiella sp. Streptomyces sp., Rhizobium sp., Escherichia sp., Pseudomonas sp., Salmonella sp., Shigella sp., Vibrio sp., Yersinia sp., Mycoplasma sp., Agrobacterium, Lactobacillus sp.). [178] The polynucleotides encoding the RGNs or crRNAs, can be used to transform any eukaryotic species, including but not limited to animals (e.g., mammals, insects, fish, birds, and reptiles), fungi, amoeba, algae, and yeast. [179] Conventional viral and non-viral based gene transfer methods can be used to introduce nucleic acids in mammalian cells or target tissues. Such methods can be used to administer nucleic acids encoding components of a CRISPR system to cells in culture, or in a host organism. Non-viral vector delivery systems include DNA plasmids, RNA (e.g. a transcript of a vector described herein), naked nucleic acid, and nucleic acid complexed with a delivery vehicle, such as a liposome. Viral vector delivery systems include DNA and RNA viruses, which have either episomal or integrated genomes after delivery to the cell. Methods of non-viral delivery of nucleic acids include lipofection, nucleofection, microinjection, biolistics, virosomes, liposomes, immunoliposomes, polycation or lipid: nucleic acid conjugates, naked DNA, artificial virions, and agent-enhanced uptake of DNA. Lipofection is described in e.g., U.S.5,049,386, 4 and lipofection reagents are sold commercially. Delivery can be to cells (e.g. in vitro or ex vivo administration) or target tissues ( e.g. in vivo administration). The preparation of lipid: nucleic acid complexes, including targeted liposomes such as immunolipid complexes, is well known to one of skill in the art (see, e.g., Gao et ah, Gene Therapy 2:710-722 (1995)). [180] The use of RNA or DNA viral based systems for the delivery of nucleic acids takes advantage of highly evolved processes for targeting a virus to specific cells in the body and trafficking the viral 35

payload to the nucleus. Viral vectors can be administered directly to patients (in vivo) or they can be used to treat cells in vitro, and the modified cells may optionally be administered to patients ( ex vivo). Conventional viral based systems could include retroviral, lentivirus, adenoviral, adeno- associated and herpes simplex virus vectors for gene transfer. Integration in the host genome is possible with the retrovirus, lentivirus, and adeno-associated virus gene transfer methods, often resulting in long term expression of the inserted transgene. Additionally, high transduction efficiencies have been observed in many different cell types and target tissues. [181] The tropism of a retrovirus can be altered by incorporating foreign envelope proteins, expanding the potential target population of target cells. Lentiviral vectors are retroviral vectors that are able to transduce or infect non-dividing cells and typically produce high viral titers. Selection of a retroviral gene transfer system would therefore depend on the target tissue. Retroviral vectors are comprised of cis-acting long terminal repeats with packaging capacity for up to 6-10 kb of foreign sequence. The minimum cis-acting LTRs are sufficient for replication and packaging of the vectors, which are then used to integrate the therapeutic gene into the target cell to provide permanent transgene expression. Widely used retroviral vectors include those based upon murine leukemia virus (MuLV), gibbon ape leukemia virus (GaLV), [182] Simian Immuno deficiency virus (SIV), human immuno deficiency virus (HIV), and combinations thereof (see, e.g., Buchscher et al., J. Viral.66:2731-2739 (1992); Johann et al., J. Viral. 66: 1635-1640 (1992); Sommnerfelt et al., Viral.176:58-59 (1990); Wilson et al., J. Viral.63:2374- 2378 (1989); Miller et al., 7. Viral.65:2220-2224 Viral delivery for therapeutic applications [183] The use viral based systems for the delivery of nucleic acids allows targeting a virus to specific cells and trafficking the viral payload to the nucleus. Viral vectors can be administered directly to patients (in vivo) or they can be used to treat cells in vitro, and the modified cells may optionally be administered to patients (ex vivo). Conventional viral based systems could include retroviral, lentivirus, adenoviral, adeno-associated and herpes simplex virus vectors for gene transfer. Integration in the host genome is possible with the retrovirus, lentivirus, and adeno-associated virus gene transfer methods, often resulting in long term expression of the inserted transgene. Additionally, high transduction efficiencies have been observed in many different cell types and target tissues. [184] The tropism of a retrovirus can be altered by incorporating foreign envelope proteins, expanding the potential target population of target cells. Lentiviral vectors are retroviral vectors that are able to transduce or infect non-dividing cells and typically produce high viral titers. Selection of a retroviral gene transfer system would therefore depend on the target tissue. Retroviral vectors are comprised of cis-acting long terminal repeats with packaging capacity for up to 6-10 kb of foreign sequence. The minimum cis-acting LTRs are sufficient for replication and packaging of the vectors, 36

which are then used to integrate the therapeutic gene into the target cell to provide permanent transgene expression. Widely used retroviral vectors include those based upon murine leukemia virus (MuLV), gibbon ape leukemia virus (GaLV), Simian Immuno deficiency virus (SIV), human immuno deficiency virus (HIV), and combinations thereof. Transient expression and gene therapy applications [185] In applications where transient expression is preferred, adenoviral based systems may be used. Adenoviral based vectors are capable of very high transduction efficiency in many cell types and do not require cell division. With such vectors, high titer and levels of expression have been obtained. This vector can be produced in large quantities in a relatively simple system. Adeno-associated virus ("AAV") vectors may also be used to transduce cells with target nucleic acids. Construction of recombinant AAV vectors are described in a number of publications, including U.S.5,173,414. Packaging cells are typically used to form virus particles that are capable of infecting a host cell. [186] Viral vectors used in gene therapy are usually generated by producing a cell line that packages a nucleic acid vector into a viral particle. The vectors typically contain the minimal viral sequences required for packaging and subsequent integration into a host, other viral sequences being replaced by an expression cassette for the polynucleotide( s) to be expressed. The missing viral functions are typically supplied in trans by the packaging cell line. For example, AAV vectors used in gene therapy typically only possess ITR sequences from the AAV genome which are required for packaging and integration into the host genome. Viral DNA is packaged in a cell line, which contains a helper plasmid encoding the other AAV genes, namely rep and cap, but lacking ITR sequences. [187] The cell line may also be infected with adenovirus as a helper. The helper virus promotes replication of the AAV vector and expression of AAV genes from the helper plasmid. The helper plasmid is not packaged in significant amounts due to a lack of ITR sequences. Contamination with adenovirus can be reduced by, e.g., heat treatment to which adenovirus is more sensitive than AAV. Additional methods for the delivery of nucleic acids to cells are known to those skilled in the art. See, for example, US20030087817 Methods of modifying target nucleotide sequence [188] In one aspect, the disclosure provides methods of modifying a target polynucleotide in a eukaryotic cell, which may be performed in vivo, ex vivo or in vitro. In some embodiments, the method comprises sampling a cell or population of cells from a human or non-human animal or plant (including microalgae) and modifying the cell or cells. Culturing may occur at any stage ex vivo. The cell or cells may even be re-introduced into the non-human animal or plant (including micro-algae). [189] The present disclosure provides methods for binding, cleaving, and/or modifying a target nucleotide sequence of interest. The methods include delivering a system comprising at least one crRNA or a polynucleotide encoding the same, and at least one RGN polypeptide or a polynucleotide 37

encoding the same to the target sequence or a cell, organelle, or embryo comprising the target sequence. In some of these embodiments, the RGN comprises the amino acid sequence set forth in Table 4, or an active variant or fragment thereof. In various embodiments, the crRNA comprises a CRISPR repeat sequence comprising the nucleotide sequence set forth in Table 5, or an active variant or fragment thereof. The RGN of the system may be nuclease dead RGN, have nickase activity, or may be a fusion polypeptide. In some embodiments, the fusion polypeptide comprises a base-editing polypeptide, for example a cytidine deaminase or an adenosine deaminase. In particular embodiments, the RGN and/or crRNA is heterologous to the cell, organelle, or embryo to which the RGN and/or crRNA (or polynucleotide(s) encoding at least one of the RGN and crRNA) are introduced. [190] In those embodiments wherein the method comprises delivering a polynucleotide encoding a crRNA and/or an RGN polypeptide, the cell, organelle, or embryo can then be cultured under conditions in which the crRNA and/or RGN polypeptide are expressed. In various embodiments, the method comprises contacting a target sequence with an RGN ribonucleoprotein complex. The RGN ribonucleoprotein complex may comprise an RGN that is nuclease dead or has nickase activity. In some embodiments, the RGN of the ribonucleoprotein complex is a fusion polypeptide comprising a base-editing polypeptide. In certain embodiments, the method comprises introducing into a cell, organelle, or embryo comprising a target sequence an RGN ribonucleoprotein complex. The RGN ribonucleoprotein complex can be one that has been purified from a biological sample, recombinantly produced and subsequently purified, or in vitro- assembled as described herein. In those embodiments wherein the RGN ribonucleoprotein complex that is contacted with the target sequence or a cell organelle, or embryo has been assembled in vitro, the method can further comprise the in vitro assembly of the complex prior to contact with the target sequence, cell, organelle, or embryo. [191] A purified or in vitro assembled RGN ribonucleoprotein complex can be introduced into a cell, organelle, or embryo using any method known in the art, including, but not limited to electroporation. [192] Alternatively, an RGN polypeptide and/or polynucleotide encoding or comprising the crRNA can be introduced into a cell, organelle, or embryo using any method known in the art (e.g., electroporation). [193] Upon delivery to or contact with the target sequence or cell, organelle, or embryo comprising the target sequence, the crRNA directs the RGN to bind to the target sequence in a sequence-specific manner. In those embodiments wherein the RGN has nuclease activity, the RGN polypeptide cleaves the target sequence of interest upon binding. The target sequence can subsequently be modified via endogenous repair mechanisms, such as non-homologous end joining, or homology-directed repair with a provided donor polynucleotide. [194] Methods to measure binding of an RGN polypeptide to a target sequence are known in the art and include chromatin immunoprecipitation assays, gel mobility shift assays, DNA pull-down assays, 38

reporter assays, microplate capture and detection assays. Likewise, methods to measure cleavage or modification of a target sequence are known in the art and include in vitro or in vivo cleavage assays wherein cleavage is confirmed using PCR, sequencing, or gel electrophoresis, with or without the attachment of an appropriate label (e.g., radioisotope, fluorescent substance) to the target sequence to facilitate detection of degradation products. Alternatively, the nicking triggered exponential amplification reaction (NTEXPAR) assay can be used (see, e.g., Zhang et al. (2016) Chem. Sci. 7:4951-4957). In vivo cleavage can be evaluated using the Surveyor assay (Guschin et al. (2010) Methods Mol Biol 649:247-256). [195] In some embodiments, the methods involve the use of a single type of RGN complexed with more than one crRNA. The more than one crRNA can target different regions of a single gene or can target multiple genes. [196] In those embodiments wherein a donor polynucleotide is not provided, a double -stranded break introduced by an RGN polypeptide can be repaired by a non-homologous end-joining (NHEJ) repair process. Due to the error-prone nature of NHEJ, repair of the double -stranded break can result in a modification to the target sequence. As used herein, a“modification” in reference to a nucleic acid molecule refers to a change in the nucleotide sequence of the nucleic acid molecule, which can be a deletion, insertion, or substitution of one or more nucleotides, or a combination thereof. Modification of the target sequence can result in the expression of an altered protein product or inactivation of a coding sequence. [197] In those embodiments wherein a donor polynucleotide is present, the donor sequence in the donor polynucleotide can be integrated into or exchanged with the target nucleotide sequence during the course of repair of the introduced double-stranded break, resulting in the introduction of the exogenous donor sequence. A donor polynucleotide thus comprises a donor sequence that is desired to be introduced into a target sequence of interest. In some embodiments, the donor sequence alters the original target nucleotide sequence such that the newly integrated donor sequence will not be recognized and cleaved by the RGN. Integration of the donor sequence can be enhanced by the inclusion within the donor polynucleotide of flanking sequences that have substantial sequence identity with the sequences flanking the target nucleotide sequence, allowing for a homology-directed repair process. In those embodiments wherein the RGN polypeptide introduces double -stranded staggered breaks, the donor polynucleotide can comprise a donor sequence flanked by compatible overhangs, allowing for direct ligation of the donor sequence to the cleaved target nucleotide sequence comprising overhangs by a non-homologous repair process during repair of the double - stranded break. [198] In those embodiments wherein the method involves the use of an RGN that is a nickase (i.e.. is only able to cleave a single strand of a double-stranded polynucleotide), the method can comprise 39

introducing two RGN nickases that target identical or overlapping target sequences and cleave different strands of the polynucleotide. For example, an RGN nickase that only cleaves the positive (+) strand of a double-stranded polynucleotide can be introduced along with a second RGN nickase that only cleaves the negative (-) strand of a double-stranded polynucleotide. [199] In various embodiments, a method is provided for binding a target nucleotide sequence and detecting the target sequence, wherein the method comprises introducing into a cell, organelle, or embryo at least one crRNA or a polynucleotide encoding the same, and at least one RGN polypeptide or a polynucleotide encoding the same, expressing the crRNA and/or RGN polypeptide (if coding sequences are introduced), wherein the RGN polypeptide is a nuclease-dead RGN and further comprises a detectable label, and the method further comprises detecting the detectable label. The detectable label may be fused to the RGN as a fusion protein (e.g., fluorescent protein) or may be a small molecule conjugated to or incorporated within the RGN polypeptide that can be detected visually or by other means. Methods of modulating gene expression [200] Also provided herein are methods for modulating the expression of a target sequence or a gene of interest under the regulation of a target sequence. The methods comprise introducing into a cell, organelle, or embryo at least one crRNA or a polynucleotide encoding the same, and at least one RGN polypeptide or a polynucleotide encoding the same, expressing the crRNA and/or RGN polypeptide (if coding sequences are introduced), wherein the RGN polypeptide is a nuclease-dead RGN. In some of these embodiments, the nuclease-dead RGN is a fusion protein comprising an expression modulator domain (i.e., epigenetic modification domain, transcriptional activation domain or a transcriptional repressor domain) as described herein. Kits [201] In one aspect, the invention provides kits containing any one or more of the elements disclosed in the above methods and compositions. In some embodiments, the kit comprises a vector system and instructions for using the kit. In some embodiments, the vector system comprises (a) a first regulatory element operably linked to a crRNA sequence and one or more insertion sites for inserting a guide sequence upstream of the crRNA sequence, wherein when expressed, the crRNA sequence directs sequence-specific binding of a RGN to a target sequence in a eukaryotic cell, wherein the RGN/RNA complex comprises an RGN complexed with the crRNA sequence that is hybridized to the target sequence, and/or (b) a second regulatory element operably linked to an enzyme coding sequence encoding said RGN comprising a nuclear localization sequence. Elements may be provided individually or in combinations, and may be provided in any suitable container, such as a vial, a bottle, or a tube. 40

[202] In some embodiments, the kit includes instructions in one or more languages. In some embodiments, a kit comprises one or more reagents for use in a process utilizing one or more of the elements described herein. Reagents may be provided in any suitable container. For example, a kit may provide one or more reaction or storage buffers. Reagents may be provided in a form that is usable in a particular assay, or in a form that requires addition of one or more other components before use (e.g. in concentrate or lyophilized form). A buffer can be any buffer, including but not limited to a sodium carbonate buffer, a sodium bicarbonate buffer, a borate buffer, a Tris buffer, a MOPS buffer, a HEPES buffer, and combinations thereof. In some embodiments, the buffer is alkaline. In some embodiments, the buffer has a pH from about 7 to about 10. [203] In some embodiments, the kit comprises one or more oligonucleotides corresponding to a crRNA sequence for insertion into a vector so as to operably link the crRNA sequence and a regulatory element. In some embodiments, the kit comprises a homologous recombination template polynucleotide. In one aspect, the invention provides methods for using one or more elements of a CRISPR system. The CRISPR complex of the invention provides an effective means for modifying a target polynucleotide. The CRISPR complex of the invention has a wide variety of utility including modifying (e.g., deleting, inserting, translocating, inactivating, activating) a target polynucleotide in a multiplicity of cell types. As such the CRISPR complex of the invention has a broad spectrum of applications in, e.g., gene therapy, drug screening, disease diagnosis, and prognosis. An exemplary CRISPR complex comprises a CRISPR enzyme complexed with a guide sequence hybridized to a target sequence within the target polynucleotide. Cells comprising the RGN systems [204] Provided herein are cells and organisms comprising a target sequence of interest that has been modified using a process or the system based an RGN and/or crRNA as described herein. Also are provided cells and organisms comprising the system for binding a target sequence of interest comprising an RGN and/or crRNA as described herein [205] In some of these embodiments, the RGN comprises the amino acid sequence as disclosed above, or an active variant or fragment thereof. In various embodiments, the crRNA comprises a CRISPR repeat sequence comprising the nucleotide sequence as disclosed above, or an active variant or fragment thereof. The modified cells can be eukaryotic (e.g., mammalian, plant, insect cell) or prokaryotic. Also provided are organelles and embryos comprising at least one nucleotide sequence that has been modified by a process utilizing an RGN and/or crRNA as described herein. The genetically modified cells, organisms, organelles, and embryos can be heterozygous or homozygous for the modified nucleotide sequence. [206] The chromosomal modification of the cell, organism, organelle, or embryo can result in altered expression (up-regulation or down-regulation), inactivation, or the expression of an altered protein 41

product or an integrated sequence. In those instances wherein the chromosomal modification results in either the inactivation of a gene or the expression of a non-functional protein product, the genetically modified cell, organism, organelle, or embryo is referred to as a “knock out”. The knock out phenotype can be the result of a deletion mutation (i.e.. deletion of at least one nucleotide), an insertion mutation (i.e.. insertion of at least one nucleotide), or a nonsense mutation (/. e. , substitution of at least one nucleotide such that a stop codon is introduced). [207] Alternatively, the chromosomal modification of a cell, organism, organelle, or embryo can produce a “knock in”, which results from the chromosomal integration of a nucleotide sequence that encodes a protein. In some of these embodiments, the coding sequence is integrated into the chromosome such that the chromosomal sequence encoding the wild-type protein is inactivated, but the exogenously introduced protein is expressed. [208] In other embodiments, the chromosomal modification results in the production of a variant protein product. The expressed variant protein product can have at least one amino acid substitution and/or the addition or deletion of at least one amino acid. The variant protein product encoded by the altered chromosomal sequence can exhibit modified characteristics or activities when compared to the wild-type protein, including but not limited to altered enzymatic activity or substrate specificity. [209] In yet other embodiments, the chromosomal modification can result in an altered expression pattern of a protein. As a non-limiting example, chromosomal alterations in the regulatory regions controlling the expression of a protein product can result in the overexpression or downregulation of the protein product or an altered tissue or temporal expression pattern. Pharmaceutical compositions [210] The composition of the present invention may be in a pharmaceutical composition. The pharmaceutical composition may comprise about 1 ng to about 10 mg of DNA encoding the CRISPR/Cas- based system or CRISPR/Cas-based system protein component, i.e., the fusion protein. The pharmaceutical composition may comprise about 1 ng to about 10 mg of the DNA of the modified lentiviral vector. The pharmaceutical composition may comprise about 1 ng to about 10 mg of the DNA of the modified AAV vector and a nucleotide sequence encoding the site-specific nuclease. The pharmaceutical compositions according to the present invention can be formulated according to the mode of administration to be used. In cases where pharmaceutical compositions are injectable pharmaceutical compositions, they are sterile, pyrogen free and particulate free. An isotonic formulation is preferably used. Generally, additives for isotonicity may include sodium chloride, dextrose, mannitol, sorbitol and lactose. In some cases, isotonic solutions such as phosphate buffered saline are preferred. Stabilizers include gelatin and albumin. In some embodiments, a vasoconstriction agent is added to the formulation. 42

[211] The composition may further comprise a pharmaceutically acceptable excipient. The pharmaceutically acceptable excipient may be functional molecules as vehicles, adjuvants, carriers, or diluents. The pharmaceutically acceptable excipient may be a transfection facilitating agent, which may include surface active agents, such as immune-stimulating complexes (ISCOMS), Freunds incomplete adjuvant, LPS analog including monophosphoryl lipid A, muramyl peptides, quinone analogs, vesicles such as squalene and squalene, hyaluronic acid, lipids, liposomes, calcium ions, viral proteins, polyanions, polycations, or nanoparticles, or other known transfection facilitating agents. [212] The transfection facilitating agent can be a polyanion, polycation, including poly-L- glutamate (LGS), or lipid. The transfection facilitating agent is poly-L-glutamate, and more preferably, the poly- L-glutamate is present in the composition for genome editing in skeletal muscle or cardiac muscle at a concentration less than 6 mg/ml. The transfection facilitating agent may also include surface active agents such as immune-stimulating complexes (ISCOMS), Freunds incomplete adjuvant, LPS analog including monophosphoryl lipid A, muramyl peptides, quinone analogs and vesicles such as squalene and squalene, and hyaluronic acid may also be used administered in conjunction with the genetic construct. In some embodiments, the DNA vector encoding the composition may also include a transfection facilitating agent such as lipids, liposomes, including lecithin liposomes or other liposomes known in the art, as a DNA-liposome mixture (see for example W09324640), calcium ions, viral proteins, polyanions, polycations, or nanoparticles, or other known transfection facilitating agents. Preferably, the transfection facilitating agent is a polyanion, polycation, including poly-L- glutamate (LGS), or lipid. [213] The sequences included in the present disclosure are shown in Tables 7-10 [214] Table 7. RGN Sequences

43

44

45

46

47

48

49

50

51

52

[215] Table 8. RGN crRNA RGN-interacting sequences (sequence preceding the spacer sequence)

[216] Table 9. RGN crRNA

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[217] Table 10. RGN CRISPR RNA consensus repeats

54

EXAMPLES Example 1. Identification of RNA-Guided Nuclease [218] Metagenomic samples were searched for open reading frames (ORFs) and those that were predicted to be genes were selected. A hidden Markov model (HMM) was used to compare the putative genes to profiles of known Cas proteins. The identified Cas genes were grouped into operons, and the operon type was determined based on the presence of known signature genes. For each genome, the CRISPR arrays were identified based on the presence of regularly spaced repeats. The subtype of each CRISPR array was predicted using machine learning. Cas operons were linked to CRISPR arrays if they were less than 10 kilobases apart. Identified repeat-arrays were then used to identify putative crRNAs. Example 2: Determination of PAM requirements for each RGN through Bacterial PAM Depletion [219] PAM requirements for each RGN were determined using a bacterial PAM depletion assay essentially adapted from Kleinstiver et al. (2015) Nature 523:481-485 and Zetsche et al. (2015) Cell 163:759-771. Briefly, two plasmid libraries (C2 and T2) were generated in a pUCl8 backbone (ampR), with each containing a distinct 23bp protospacer (target) sequence flanked by 8 random nucleotides (i.e., the PAM region). The target sequence and flanking PAM region of library T2 and library C2 for each RGN are set forth in Table 11. [220] Table 11. Library tag sequences

[221] The libraries were separately electroporated into T7 Express E. coli (NEB) cells harboring pET28b expression vectors containing an RGN of the invention (codon optimized for E. coli) along with a cognate sgRNA containing a spacer sequence corresponding to the protospacer in C2 or T2. 55

Sufficient library plasmid was used in the transformation reaction to obtain >10^8 cfu. Both the RGN and crRNA in the pET28b backbone were under the control of T7 promoters. The transformation reaction was allowed to recover for 1 hr after which it was diluted into LB media containing carbenicillin and kanamycin and grown overnight. The following day the mixture was diluted into self-inducing Overnight Express™ Instant TB Medium (Millipore Sigma) to allow expression of the RGN and crRNA, and grown for an additional 4h at 37C and then shifted to 30C for an additional 16h after which the cells were spun down and plasmid DNA was isolated with a Mini-prep kit (Qiagen, Germantown, MD). In the presence of the appropriate crRNA, plasmids containing a PAM that is recognizable by the RGN will be cleaved resulting in their removal from the population. Plasmids containing PAMs that are not recognizable by the RGN, or that are transformed into bacteria not containing an appropriate crRNA, will survive and replicate. The PAM and protospacer regions of uncleaved plasmids were PCR-amplified and prepared for sequencing following published protocols (l6s-metagenomic library prep guide 15044223B, Illumina, San Diego, CA). Deep sequencing (55bp paired end reads) was performed on a NextSeq (Illumina). Typically, 1-4M reads were obtained per amplicon. PAM regions were extracted, counted, and normalized to total reads for each sample. PAMs that lead to plasmid cleavage were identified by being underrepresented when compared to controls (i.e., when the library is transformed into E. coli containing the RGN but lacking an appropriate sgRNA). To identify the PAM requirements for a novel RGN, an enrichment value was computed for each kmer as the difference between the library size-normalized read counts in the control sample and in the targeting sample. This value was rounded to the nearest integer for positive numbers and set to zero for negative numbers. Enrichment values were then summed across all kmers to yield a position frequency matrix, which was represented visually as a sequence logo using the command line utility weblogo. Those RGNs with consistency among the most enriched kmers— sequence logo information content > 0.2 when including the top 100 enriched kmers—and with qualitatively consistent PAMs across plasmid libraries (T2 and C2) were deemed to have bonafide PAMs. The final PAM for these RGNs were obtained by summing counts across both plasmid libraries, normalizing counts, computing kmer enrichment values, summing across kmers to yield a position frequency matrix, then visually representing the PAM as a sequence logo using the command line utility weblogo. Example 3: Demonstration of gene editing activity on endogenous targets in mammalian cells [222] The RGN was codon optimized for human expression and cloned into expression cassettes with a Nterm SV40 NLS, and a Cterm Nucleoplasmin NLS under control of a CMV promoter for mammalian expression. NLS tag sequences are set forth in Table 12. [223] Table 12. NLS tag sequences

56

[224] . The gRNA expression constructs encoding a single gRNA each under the control of a human RNA polymerase III U6 promoter were produced and introduced into an expression vector containing GFP under control of a CMV promoter. Guides were design to targeted regions of selected genes with the appropriate PAM for the system. The constructs described were introduced into mammalian cells. One day prior to transfection, HEK293T cells (Sigma) were plated in 24-well dishes in Dulbecco’s modified Eagle medium (DMEM) plus 10% (vol/vol) fetal bovine serum (Gibco) and 1% Penicillin- Streptomycin (Gibco). The next day when the cells were at 50-60% confluency, 500 ng of a RGN expression plasmid plus 500 ng of a single gRNA expression plasmid were co-transfected using 1.5 uL of Lipofectamine 3000 (Thermo Scientific) per well, following the manufacturer’s instructions. After 48 hours of growth, total genomic DNA was harvested using a genomic DNA isolation kit (Machery-Nagel) according to the manufacturer’s instructions. [225] The total genomic DNA was then analyzed to determine the rate of editing in the targeted gene. Oligonucleotides were produced to be used for PCR amplification and subsequent analysis of the amplified genomic target site. All PCR reactions were performed using 10 uL of 2X Master Mix Platinum SuperFi DNA polymerase (Thermo Scientific) in a 20 uL reaction including 0.5 uM of each primer specific for each guide using a program of: 98°C, 1 min; 35 cycles of [98°C, 10 sec; 65°C, 15 sec; 72°C, 30 sec]; 72°C, 5 min; 12°C, forever. Primers for PCR#2 include Nextera Read 1 and Read 2 Transposase Adapter overhang sequences for Illumina sequencing. [226] Following the PCR amplification, DNA was cleaned using a PCR cleanup kit (Zymo) according to the manufacturer’s instructions and eluted in water. Products containing the Illumina overhang sequences underwent library preparation following the Illumina 16S Metagenomic Sequencing Library protocol. Deep sequencing was performed on an Illumina NextSeq platform. Typically, 200,000 of 150 bp paired-end reads (2 x 100,000 reads) are generated per amplicon. The reads were analyzed using CRISPResso (Pinello, et al.2016 Nature Biotech, 34:695-697) to calculate the rates of editing. Output alignments were hand-curated to confirm insertion and deletion sites as well as identify microhomology sites at the recombination sites. The overall rates of editing for actively edited samples are shown in Table 13. [227] Table 13. Active Eukaryotic Editing

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Example 4: Demonstration of base editing activity on endogenous targets in mammalian cells [228] The coding sequence of the identified RGN is codon-optimized for expression in mammalian cells and introduced into the expression cassette, which produces a fusion protein that includes a NLS tag at its N-terminal end operably linked to a codon optimized known eukaryotic deaminase sequence (APOBEC3A) at its C-terminal end. The deaminase is operably linked to a flexible amino acid linker at their C-terminal end, and the amino acid linker is operably linked to the RNA guided nuclease at its C-terminal end, that has been mutated to have an inactive RuvC domain (dEGS0081_ D956A_E1050A_D1291A). The RNA-guided DNA binding polypeptide is operably linked to a flexible amino acid linker at their C-terminal end, and the amino acid linker is operably linked to a uracil protecting peptide. The uracil protecting peptide (developed in-house) is operably linked to a flexible amino acid linker at their C-terminal end, and the amino acid linker is operably linked to a second NLS at its C-terminal end. Each of these expression cassettes is introduced into a vector capable of driving the expression of the fusion protein in mammalian cells. A vector capable of expressing crRNA to target 62

the deaminase-RGN-UPP fusion protein to the determined genomic location was also produced. These crRNAs can guide the deaminase-RGN-UPP fusion protein to the target genome sequence for base editing. [229] Using liposome transfection, vectors capable of expressing the deaminase-RGN-UPP fusion protein and guide RNAs were transfected into HEK293T cells. For liposome transfection, the day before transfection, the cells were distributed in a 24-well plate of growth medium (DMEM + 10% fetal bovine serum + 1% penicillin/streptomycin) at 1.3×10⁵ cells/well. According to the manufacturer's instructions, use Lipofectamine® 3000 reagent (Thermo Fisher Scientific) to transfect 500 ng deaminase-RGN fusion expression vector and 500 ng guide RNA expression vector.48-72 hours after liposome transfection, genomic DNA is harvested from the transfected cells, and the DNA is sequenced and analyzed for the presence of targeted cytosine base editing mutations using CRISPResso2 (Clement K, et al Nat Biotechnol. 2019 Mar; 37(3):224-226. doi: 10.1038/s41587-019-0032-3. PubMed PMID: 30809026). [230] Tables 14-16 show the editing rate of cytidine bases and INDEL formation for each deaminase- RGN-UPP and the rate for targeted cytosine deamination for the deaminase-RGN-UPP targeted to the same region as the dRGN-UPP construct. Active cytosine base editing was defined as an increase of C>D SNP base editing along the targeted window of the deaminase-RGN-UPP under investigation, and >75% C>T SNP base editing at highly mutated cytosines. Without an active nuclease domain, the RGN will not function as a nuclease and will not generate a detectable INDEL formation by itself. When fused with an active deaminase that acts on the opposite strand a cytosine will be turned into a uracil. The uracil is rapidly removed from the DNA leaving an abasic site, and eventually a gap, on the strand opposite the strand bound by the crRNA. This can result in a double stranded break which is repaired through non-homologous end joining (NHEJ) and detectable INDEL formation, however, with the presence of an active UPP, the converted uracil is protected from removal and the abasic site is never removed and NHEJ does not occur. This also leads to predominantly C>T conversions because the uracil created by the deaminase is protected and not removed before the opposing strand is replicated, it will be read as a thymine when the opposing strand is replicated, and an adenosine will be inserted across from it. Then when the uracil is removed, it will be replaced by thymine during the excision repair process fixing the mutation at C>T. [231] Table 14. INDEL and Max Base editing results for deaminase-RGN-UPP constructs.

[232] Table 15. EGsG0509 editing results 63

[233] Table 16. EGsG0515 editing results

Example 5: Engineered Cas12a variants with increased activities and improved targeting ranges [234] To test if the performance of Cas12a candidates could be further improved, residues homologous to those known to create an enhanced version of AsCas12 (enAsCas12a; E174R_S542R_K548R) were identified and introduced into EGS0081 (Q158R_S528R_K535R), EGS0087 (E165R_D584R_K590R), and EGS0068 (Q167R_N575R_K581R). Multiple targets were then tested with a variety of PAMs in HEK293T cells and performance was improved for EGS0087 and EGS0068, but the mutations impaired activity in EGS0081. Initially, EGS0068 and EGS0087 showed higher performance on targets with a YTTN PAM compared to RTTN PAM, but with the enhanced versions, we saw improved activity at both RTTN and YTTN PAMs, indicating improved performance across both preferred and non-preferred targets (Figure 2). Example 6: CRISPR Activation with Cas12a variants [235] The enhanced version of EGS0087 was rendered catalytically dead (SEQ ID NO: 375) and codon optimized for human expression and cloned into expression cassettes with a Nterm FLAGtag 64

and SV40 NLS and a Cterm Nucleoplasmin NLS and a VPR activation domain under control of a hUbC promoter for mammalian expression. With a mutated catalytic domain, the Cas12a construct will not be able to cleave the dsDNA but will still bind to the dsDNA in the presence of a targeting crRNA. While bound to the DNA, the fused activator domains will recruit expression proteins to the same location and increase expression of the targeted gene of interest. Tag sequences are set forth in Table 12 and activator domain sequence in Table 19. [236] A vector capable of expressing a single crRNA guide under the control of a human RNA polymerase III U6 promoter was produced and introduced into an expression vector containing GFP under control of a CMV promoter. Guides were design to targeted regions upstream of selected genes with the appropriate PAM for the system, thereby directing the fusion protein to the targeted gene. The constructs described were introduced into mammalian cells. On day of transfection, K562 cells (Sigma) were combined with SF Nucleofector solution (Lonza) and 600 ng of a RGN expression plasmid plus 500 ng of a single crRNA expression plasmid and nucleofected at FF120 per manufactures protocol (Lonza) and plated in duplicate 96-well dishes in Dulbecco’s modified Eagle medium (RPMI) plus 10% (vol/vol) fetal bovine serum (Gibco) and 1% Penicillin-Streptomycin (Gibco). After 72 hours of growth, cells were washed and harvested in PBS+1% BSA and stained with APC-labeled target specific antibody (BioLegend). Samples were run on Aria (BD). [237] Table 17 shows the % increase of the expressed targeted protein for the gene in interest. Successful gene activation was defined as at least a 3-fold increase in the detectable amount of targeted protein. [238] Table 17. CRISPR Activation using dEGS0087_E165R_D584R_K590R_D968A_VPR

[239] Table 18. Mutated RGN Sequences

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Claims

WHAT IS CLAIMED IS: 1. A nucleic acid targeting system, comprising a) a polypeptide comprising an RNA-guided nuclease (RGN) protein comprising an amino acid sequence that is at least 80% identical to the amino acid sequence set forth in any one of SEQ ID NO: 1-27, and b) an RNA molecule binding to RNA-guided nuclease protein (crRNA) and targeting a nucleic acid sequence of interest, said crRNA comprising in 5’ to 3’ orientation: i. a first region that binds to the RGN, and ii. a second region comprising a spacer sequence complimentary to the target nucleic acid sequence of interest.

2. The nucleic acid targeting system of claim 1, wherein the target nucleic acid is a DNA.

3. The nucleic acid targeting system of claim 1, wherein the first region that binds to the RGN comprises a part of the corresponding CRISPR repeat sequence capable of forming a hairpin structure.

4. The nucleic acid targeting system of claim 1, wherein the first region that binds to the RGN comprises a sequence of any of SEQ ID NO: 28-54 or a variant thereof capable of forming a hairpin structure.

5. The nucleic acid targeting system of claim 1, wherein the crRNA comprises has the sequence of SEQ ID NO: 55-81 respectively.

6. The nucleic acid targeting system of claim 1, wherein the target sequence is adjacent to a PAM sequence.

7. The nucleic acid targeting system of claim 1, wherein said RGN polypeptide is a nickase or nuclease dead.

8. The nucleic acid targeting system of claim 1, wherein the target nucleic acid sequence is within a eukaryotic cell.

9. The nucleic acid targeting system of claim 1, wherein said RGN polypeptide is nuclease dead, and wherein the RGN polypeptide is operably linked to a base-editing polypeptide.

10. The nucleic acid targeting system of claim 9, wherein said base-editing polypeptide is a cytidine base editor.

11. One or more isolated polynucleotides encoding the nucleic acid targeting system of any one of claims 1-10.

12. The isolated polynucleotides of claim 11, wherein the polynucleotide sequences encoding of the nucleic acid targeting system have been codon optimized for optimal expression in a target cell or organism. 72

13. One or more vectors comprising one or more isolated polynucleotides of claim 11.

14. The one or more vectors of claim 13, wherein said vector is a lentiviral or an AAV vector.

15. A vector comprising polynucleotides encoding said nucleic acid targeting system of any one of claims 1-10.

16. The vector of claim 15, wherein said vector is a lentiviral or an AAV vector.

17. A cell comprising the nucleic acid targeting system of any one of claims 1-10, the polynucleotide of claim 11, or the vector of claim 13 or 15.

18. A cell according to claim 17, wherein said cell is an eucaryotic cell.

19. A composition comprising the DNA targeting system of any one of claims 1-10, one or more polynucleotides of claim 11, or one or more vectors of claim 13 or 15.

20. A method for binding to a target DNA sequence comprising contacting the DNA targeting system according to any one of claims 1-10, with said target DNA sequence or a cell comprising the target DNA sequence.

21. A method for cleaving and/or modifying a target nucleic acid sequence, comprising 1) contacting the target nucleic acid sequence with a nucleic acid targeting system of any one of claims 1-10; and 2) incubating said nucleic acid targeting system with the target nucleic acid for the time and under conditions sufficient for the cleaving and/or modification to occur.

22. The method of claim 21, wherein said target nucleic acid sequence is a DNA.

23. The method of claim 21, wherein said modified target DNA sequence comprises insertion of heterologous nucleic acid sequence into the target DNA sequence.

24. The method of claim 21, wherein said modified target DNA sequence comprises deletion of at least one nucleotide from the target DNA sequence

25. The method of claim 21, wherein said modified target DNA sequence comprises mutation of at least one nucleotide in the target DNA sequence

26. The method of claim 21, wherein the target nucleic acid sequence is within a cell.

27. The method of claim 26, wherein the cell is a eukaryotic cell.

28. The method of claim 21, further comprising culturing the cell under conditions sufficient for expression of the RGN polypeptide and selecting a cell comprising said modified target nucleic acid sequence. 73

29. A pharmaceutical composition comprising the nucleic acid targeting system of any one of claims 1-10, one or more polynucleotides of claim 11, or one or more vectors of claim 13 or 15. 74