WO2024032678A1 - Procédé d'édition d'épigénome de cibles et son utilisation - Google Patents

Procédé d'édition d'épigénome de cibles et son utilisation Download PDF

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WO2024032678A1
WO2024032678A1 PCT/CN2023/112094 CN2023112094W WO2024032678A1 WO 2024032678 A1 WO2024032678 A1 WO 2024032678A1 CN 2023112094 W CN2023112094 W CN 2023112094W WO 2024032678 A1 WO2024032678 A1 WO 2024032678A1
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molecule
gene expression
nucleic acid
gene
sequence
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PCT/CN2023/112094
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English (en)
Chinese (zh)
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张宝弘
罗浩
韦翔
王鹏程
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益杰立科(上海)生物科技有限公司
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression

Definitions

  • This application relates to the field of biomedicine, specifically to an epigenetic editing target and its use.
  • Targeting this target can be used to improve the effect and safety of epigenetic editing and reduce toxicity, immunogenicity and/or off-target effects.
  • the present application provides an epigenetic editing target.
  • Targeting the target can be used to improve the epigenetic editing effect and safety, and reduce toxicity, immunogenicity and/or off-target effects.
  • targeting near the target gene and/or within the target gene regulatory element can effectively modify at least one nucleotide, thereby regulating (eg, reducing or eliminating) the expression of the target gene product in the cell.
  • the present application provides a method for regulating F11 (Coagulation Factor XI) gene expression and/or activity.
  • the method includes providing a gene expression regulatory molecule or a nucleic acid encoding the gene expression regulatory molecule.
  • the gene The expression regulatory molecule has the function of regulating the expression of the F11 gene without changing its gene sequence.
  • the present application provides a method for treating and/or alleviating conditions associated with abnormal F11 gene expression and/or F11 gene activity, the method comprising providing a gene expression regulatory molecule or encoding the gene expression regulator
  • the nucleic acid of the molecule, the gene expression regulating molecule has the function of regulating the expression of the F11 gene without changing its gene sequence.
  • the gene expression modulating molecule comprises a DNA binding domain.
  • the gene expression regulatory molecule comprises one or more DNA binding domains selected from the group consisting of TALEN domains, zinc finger domains, and protein domains of the CRISPR/Cas system.
  • the gene expression regulatory molecule comprises a Cas enzyme.
  • the gene expression modulating molecule comprises a Cas enzyme that has substantially no nuclease activity.
  • the gene expression modulating molecule comprises a dCas9 enzyme.
  • the gene expression regulatory molecule is capable of binding to a DNA region or a fragment thereof within 500 bp upstream and/or downstream of the transcription start site (TSS) of the F11 gene.
  • TSS transcription start site
  • the gene expression regulatory molecule is capable of binding to the DNA region located in any one of SEQ ID NOs: 71-72 or a fragment thereof.
  • the gene expression regulatory molecule can bind to one or more DNA regions near the transcription start site (TSS) of the F11 gene: between 250 bp upstream of the TSS and 130 bp upstream of the TSS. Between 50bp upstream and 120bp downstream, and between 230bp downstream and 390bp downstream of TSS.
  • TSS transcription start site
  • the gene expression regulatory molecule can bind to one or more DNA regions near the transcription start site (TSS) of the F11 gene: between 250 bp upstream of the TSS and 230 bp upstream of the TSS. Between 210bp upstream and 180bp upstream, between 160bp upstream and 130bp upstream of TSS, between 50bp upstream and 10bp downstream of TSS, between 30bp downstream and 60bp downstream of TSS, between 90bp and 120bp downstream of TSS, and Between 230bp downstream and 260bp downstream, between 300bp downstream and 320bp downstream of TSS, and between 360bp downstream and 390bp downstream of TSS.
  • TSS transcription start site
  • the methods include providing a nucleic acid binding molecule comprising the sequence of any one of SEQ ID NOs: 1-70.
  • the gene expression modulating molecule and/or the nucleic acid binding molecule are formulated in the same or different delivery vehicles.
  • the delivery vehicle comprises liposomes and/or lipid nanoparticles.
  • the gene expression modulating molecule and/or the nucleic acid binding molecule are formulated in the same or different recombinant vectors.
  • the recombinant vector comprises a viral vector.
  • the recombinant vector comprises an adeno-associated virus (AAV) vector.
  • AAV adeno-associated virus
  • the gene expression modulating molecule comprises a first functional domain that provides modification of at least one nucleotide near the F11 gene and/or within the F11 gene regulatory element.
  • the modification of at least one nucleotide comprises a methylation modification.
  • the regulatory elements comprise a core promoter, a proximal promoter, a distal enhancer, a silencer, an insulator element, a border element, and/or a locus control region.
  • the first functional domain includes a DNA methyltransferase, a DNA demethylase, and a functional One or more active fragments.
  • the DNA methyltransferase comprises one or more of DNMT 3A, DNMT 3B, DNMT 3L, DNMT1 and DNMT 2.
  • the DNMT 3A is derived from mice.
  • the DNMT 3L is derived from human and/or mouse.
  • the DNMT 3A and the DNMT 3L are directly and/or indirectly connected.
  • the gene expression modulating molecule comprises a second functional domain comprising a zinc finger protein-based transcription factor or a functionally active fragment thereof, or a substance capable of modifying histones.
  • the second functional domain includes Krab.
  • the second functional domain comprises ZIM3 Krab or KOX1 Krab.
  • the second functional domain comprises one of a histone methyltransferase, a histone demethylase, a histone acetyltransferase, a histone deacetylase, and functionally active fragments thereof, or Various.
  • the first functional domain and the second functional domain are directly or indirectly linked to one end of the DNA binding domain.
  • the gene expression modulating molecule comprises a nuclear localization sequence.
  • the nuclear localization sequence comprises an amino acid having an electropositive group.
  • the nuclear localization sequence is located at the N-terminus and/or C-terminus of the first functional domain, the N-terminus and/or C-terminus of the second functional domain, and/or the DNA binding domain N-terminus and/or C-terminus.
  • the present application provides a nucleic acid binding molecule comprising the sequence of any one of SEQ ID NOs: 1-70.
  • the present application provides a gene expression regulatory molecule that has the function of regulating the expression of the F11 gene without changing its gene sequence.
  • the gene expression modulating molecule is as provided in the methods of the present application.
  • the gene expression modulating molecules and/or nucleic acid binding molecules comprising the sequence of any one of SEQ ID NOs: 1-70 are formulated in the same or different delivery vectors.
  • the delivery vehicle comprises liposomes and/or lipid nanoparticles.
  • the expression modulating molecule and/or the nucleic acid binding molecule comprising the sequence of any one of SEQ ID NOs: 1-70 is formulated in the same or different recombinant vectors.
  • the recombinant vector comprises a viral vector.
  • the recombinant vector comprises an adeno-associated virus (AAV) vector.
  • AAV adeno-associated virus
  • the present application provides a nucleic acid encoding the nucleic acid binding molecule of the present application and/or encoding the gene expression regulating molecule of the present application.
  • the present application provides a recombinant vector comprising the nucleic acid of the present application.
  • the present application provides a delivery vector, the delivery vector comprising the nucleic acid binding molecule of the present application, the gene expression regulatory molecule of the present application, the nucleic acid of the present application, and/or the recombinant vector of the present application, and optionally containing liposomes and/or lipid nanoparticles.
  • the present application provides a composition comprising the nucleic acid binding molecule of the present application, the gene expression regulating molecule of the present application, the nucleic acid of the present application, the recombinant vector of the present application, and/or the present application. Delivery vehicle.
  • the present application provides a cell comprising the nucleic acid binding molecule of the present application, the gene expression regulating molecule of the present application, the nucleic acid of the present application, the recombinant vector of the present application, the delivery vector of the present application, and/ or compositions of the present application.
  • the present application provides a kit, which includes the nucleic acid binding molecule of the present application, the gene expression regulating molecule of the present application, the nucleic acid of the present application, the recombinant vector of the present application, the delivery vector of the present application, The composition of the present application, and/or the cell of the present application.
  • the present application provides a method for regulating the expression and/or activity of a target gene, which method includes providing the nucleic acid binding molecule of the present application, the gene expression regulating molecule of the present application, the nucleic acid of the present application, and the recombinant of the present application.
  • the present application provides a nucleic acid binding molecule of the present application, a gene expression regulating molecule of the present application, a nucleic acid of the present application, a recombinant vector of the present application, a delivery vector of the present application, a composition of the present application, and a nucleic acid binding molecule of the present application.
  • the application of the cells and/or the kit of the present application in the preparation of medicaments for treating and/or alleviating disorders, including disorders associated with abnormal expression and/or activity of target genes.
  • Figure 1A shows a schematic diagram of the reporter plasmid constructed from the F11 gene fragment and fluorescent protein.
  • Figure 1B shows the flow cytometry results of the proportion of cells with low green fluorescence intensity in the transfected cell population.
  • Figure 1C shows the expression regulatory effect of the gene expression regulatory molecule of the present application in targeting different F11 gene regulatory regions.
  • nucleic acid is used interchangeably with “polynucleotide”, “nucleotide”, “nucleotide sequence” and “oligonucleotide”, which generally refers to nucleotides (e.g. , deoxyribonucleotides or ribonucleotides) and their polymers in single-stranded, double-stranded or multi-stranded form or their complements.
  • nucleotides may be ribonucleotides, deoxyribonucleotides, or modified versions thereof.
  • nucleotides can be single- and double-stranded DNA, single- and double-stranded RNA, and hybrid molecules with mixtures of single- and double-stranded DNA and RNA.
  • nucleotides may include, but are not limited to, any type of RNA, such as mRNA, siRNA, miRNA, sgRNA, and guide RNA, as well as any type of DNA, genomic DNA, plasmid DNA, and minicircle DNA, and any fragments thereof.
  • the term also encompasses nucleic acids, whether synthetic, naturally occurring and non-naturally occurring, containing known nucleotide analogs or modified backbone residues or linkages.
  • sequence encoding or “nucleic acid encoding” generally refers to a nucleic acid (RNA or DNA molecule) comprising a nucleotide sequence encoding a protein.
  • the coding sequence may also include initiation and termination signals operably linked to regulatory elements comprising a promoter and a polyadenylation signal capable of directing expression in cells of an individual or mammal to which the nucleic acid is administered. .
  • the coding sequence can be codon optimized.
  • treatment for example, when applied to a disease, means when administering, for example, a gene expression modulating molecule as described herein or a nucleic acid encoding such a gene expression modulating molecule and/or a nucleic acid binding molecule as described herein (for example, gRNA) or a nucleic acid encoding the nucleic acid binding molecule, compared with when the gene expression regulating molecule or the nucleic acid encoding the gene expression regulating molecule and/or the nucleic acid binding molecule or the nucleic acid encoding the nucleic acid binding molecule has never been administered,
  • a subject eg, a human who has the disease, is at risk for the disease, and/or experiences symptoms of the disease will, in one embodiment, experience milder symptoms and/or will recover more quickly.
  • DNA-binding domain generally refers to an independently folded protein domain containing at least one motif that recognizes double-stranded or single-stranded DNA.
  • the DNA binding domain may recognize a specific DNA sequence (recognize or modulate sequence) or have general affinity for DNA.
  • other domains of the DNA-binding domain often modulate the activity of the DNA-binding domain; the DNA-binding function can be structural or include transcriptional regulation, and sometimes the two roles overlap.
  • the DNA binding domain may comprise a (DNA) nuclease, such as one capable of targeting DNA in a sequence-specific manner or capable of being directed or instructed to act in a sequence-specific manner.
  • Nucleases that target DNA in a sexual manner such as the CRISPR-Cas system, zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), or meganucleases.
  • the DNA binding domain is a DNA nuclease derived from the CRISPR-Cas system.
  • the DNA nuclease derived from the CRISPR-Cas system is a Cas protein.
  • Cas enzyme may be used with “Cas protein”, “CRISPR protein”, “CRISPR enzyme”, “CRISPR-Cas protein”, “CRISPR-Cas enzyme”, “Cas”, “CRISPR effector” or “Cas effector proteins” are used interchangeably and generally refer to a class of enzymes that are complementary to CRISPR sequences and are able to use the CRISPR sequences as guides to recognize and cut specific DNA strands.
  • Cas proteins include: Casl, CaslB, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csnl and Csxl2), CaslO, Csyl, Csy2, Csy3, Csel, Cse2, Cscl , Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csxl7, Csxl4, CsxlO, Csxl6, CsaX, Csx3, Csxl, Csxl5, Cs f1 , Csf2, Csf3, Csf4, and/or their homologues, or modified forms thereof.
  • These proteins are known, for example, the amino acid sequence of the Streptococcus pyogen
  • dCas9 enzyme is also referred to as “inactivated Cas9 protein” or “inactivated Cas9 enzyme”.
  • inactivated Cas9 protein or “inactivated Cas9 enzyme”.
  • known methods for generating Cas9 proteins (or fragments thereof) with inactive DNA cleavage domains are described, for example, Jinek et al., Science. 337:816-821 (2012); Qi et al., "Repurposing CRISPR as an RNA-GuidedPlatform” for Sequence-Specific Control of Gene Expression," Cell. 28, 152(5):1173-83 (2013), the entire contents of which are incorporated herein by reference).
  • the DNA cleavage domain of Cas9 is known to include two subdomains, the HNH nuclease subdomain and the RuvC1 subdomain.
  • the HNH subdomain cleaves the strand complementary to the gRNA, while the RuvC1 subdomain cleaves the non-complementary strand. Mutations in these subdomains silence the nuclease activity of Cas9.
  • mutations D10A and H840A completely inactivate the nuclease activity of Streptococcus pyogenes Cas9 (Jinek et al., Science. 337:816-821 (2012); Qi et al., Cell. 28; 152(5): 1173-83 ( 2013)).
  • Suitable CRISPR inactivating or nicking DNA binding domains include, but are not limited to, nuclease inactive variant Cas9 domains including D10A, D10A/D839A/H840A and D10A/D839A/H840A/N863A mutant domains, such as WO2015089406A1 , which is incorporated herein by reference.
  • endonuclease-inactive dCas9 from Streptococcus pyogenes has been targeted by gRNA to genes in bacteria, yeast, and human cells to silence gene expression through steric hindrance.
  • dCas may refer to a dCas protein or fragment thereof.
  • dCas9 may refer to a dCas9 protein or fragment thereof.
  • the term “iCas” Used interchangeably with “dCas” to refer to CRISPR-related proteins that have no catalytic activity.
  • the dCas protein contains one or more mutations in the DNA cleavage domain.
  • the dCas protein contains one or more mutations in the RuvC or domain.
  • the dCas molecule contains one or more mutations in both the RuvC and HNH domains.
  • the dCas protein is a fragment of wild-type Cas protein.
  • the dCas protein comprises a functional domain from a wild-type Cas protein, wherein the functional domain is selected from the group consisting of a Reel domain, a bridged helix domain, or a PAM interaction domain.
  • the nuclease activity of dCas is reduced by at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65% compared to the nuclease activity of the corresponding wild-type Cas protein. , at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99%.
  • Suitable dCas can be derived from wild-type Cas protein.
  • Cas proteins can be derived from type I, type II, or type III CRISPR-Cas systems.
  • a suitable dCas may be derived from Cas1, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 or Cas10.
  • dCas is derived from Cas9 protein.
  • dCas9 can be obtained by introducing point mutations (eg, substitutions, deletions or additions) in the DNA cleavage domain (eg, nuclease domain, eg, RuvC and/or HNH domain) of the Cas9 protein.
  • introducing two point mutations in the RuvC and HNH domains reduced Cas9 nuclease activity while retaining Cas9 sgRNA and DNA binding activities.
  • the two point mutations within the RuvC and HNH active sites are the D10A and H840A mutations of S. pyogenes Cas9.
  • D10 and H840 of S. pyogenes Cas9 can be deleted to eliminate Cas9 nuclease activity while retaining its sgRNA and DNA binding activities.
  • the two point mutations within the RuvC and HNH active sites are the D10A and N580A mutations of S. pyogenes Cas9.
  • the present application relates to a dCas protein, or any variant or mutant thereof.
  • All variants and mutants of dCas9 including but not limited to those derived from SpCas9 (Cas9 isolated from Streptococcus pyogenes), SaCas9 ( Cas9 isolated from Staphylococcus aureus), StCas9 (Cas9 isolated from Streptococcus thermophilus), NmCas9 (Cas9 isolated from Neisseria meningitidis), FnCas9 (Cas9 isolated from Francisella novicida isolated Cas9), CjCas9 (Cas9 isolated from Campylobacter jejuni), ScCas9 (Cas9 isolated from Streptococcus canis), and any variants and mutant forms of Cas9 listed above, such as high-fidelity Cas9 ( Kleinstiver et al., Nature.
  • the dCas9 sequences shown in SEQ ID NOs: 1162-1179 of this application only provide a few exemplary options and are not exclusive.
  • the dCas protein is Streptococcus pyogenes dCas9 comprising mutations at D10 and/or H840 (as set forth in SEQ ID NO: 1162) protein.
  • the dCas protein is a Streptococcus pyogenes dCas9 protein comprising the D10A and/or H840A mutations (as set forth in SEQ ID NO: 1162).
  • the dCas9 protein is a Staphylococcus aureus dCas9 protein comprising the amino acid sequence set forth in SEQ ID NO: 1163 or 1164, substantially identical to SEQ ID NO: 1163 or 1164 (e.g., at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or higher sequence identity) sequence, or a sequence having 1, 2, 3, 4, 5 or more changes (eg, amino acid substitutions, insertions, or deletions) relative to SEQ ID NO: 11631164, or any fragment thereof.
  • dCas9 includes Streptococcus pyogenes dCas9, Staphylococcus aureus dCas9, Campylobacter jejuni dCas9, Corynebacterium diphtheria dCas9, E.
  • the application also provides vectors comprising nucleotides encoding the following protein molecules: Streptococcus pyogenes dCas9, Staphylococcus aureus dCas9, Campylobacter jejuni dCas9, Corynebacterium diphtheriae dCas9, Eubacterium aureus dCas9 dCas9, Streptococcus pasteurianus dCas9, Lactobacillus sausage dCas9, Coccidioides dCas9, Azospirillum (strain B510) dCas9, Gluconacetobacter diazophila dCas9, Neisseria griseus dCas9, R.
  • intestinalis bacterium dCas9 food detergent Corynebacterium parvum dCas9, brine nitrate lysing bacterium (strain DSM 16511) dCas9, Campylobacter gullum (strain CF89-12) dCas9, Streptococcus thermophilus (strain LMD-9) dCas9 or the above fragment.
  • the term "Cas enzyme having substantially no nuclease activity” generally refers to an RNA-guided enzyme in which recognition of phosphodiester bonds is facilitated by a separate polynucleotide sequence (e.g., guide RNA), However, the enzyme may not significantly cleave the target phosphodiester bond (eg, no measurable phosphodiester bond cleavage under physiological conditions).
  • a nuclease-deficient RNA-guided DNA endonuclease retains DNA-binding ability (e.g., specific binding to a target sequence) but lacks significant intranuclease binding.
  • nuclease-deficient RNA-guided DNA endonucleases are dCas9, ddCpf1, nuclease-deficient Cas9 variants, or nuclease-deficient Cas9 endonucleases.
  • Class II CRISPR endonuclease For example, an RNA-guided DNA endonuclease lacking nuclease is dCas9.
  • dCas9 or "dCas9 protein” as referred to herein is a Cas9 protein in which both catalytic sites of endonuclease activity are defective or lack activity.
  • dCas9 has essentially no detectable endonuclease (eg, endodeoxyribonuclease) activity.
  • dCas9 comprises at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90% of the dCas9 enzyme sequence of the present application.
  • a variant of the amino acid sequence that has %, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% sequence identity, or homologues.
  • the term “capable of binding” is used interchangeably with “binds to”, “specifically recognizes”, “targets”, etc., and generally refers to a binding molecule (e.g., a gene expression modulating molecule of the present application) Able to interact with nucleotides on the target gene or target site, or the binding molecule (for example, the gene expression regulatory molecule of the present application) has sufficient affinity for the target gene or target site.
  • This interaction can be through Conjugation, coupling, attachment, providing complementarity, providing covalent force or non-covalent force, improving binding stability, etc.
  • transcription start site generally refers to the nucleic acid in the construct that corresponds to the first nucleic acid integrated into the primary transcript (i.e., pre-mRNA); the transcription start site may Overlaps with promoter sequence.
  • fragment thereof generally refers to a portion or fragment of the specified whole.
  • fragment thereof refers to a contiguous length of a specified nucleotide sequence that is shorter than the full-length sequence of a specified polynucleotide.
  • a portion of a specified nucleotide may be defined by its first position and its last position, wherein the first and last positions each correspond to a position in the sequence of the specified polynucleotide, wherein the sequence corresponding to the first position The position is N-terminal to the sequence position corresponding to the last position, and thus the sequence of that portion is a contiguous sequence of nucleotides in the specified polynucleotide that begins at the sequence position corresponding to the first position and ends at the sequence position corresponding to the last The sequence position of the position ends.
  • a portion may also be defined by reference to a position in a specified polynucleotide sequence and the length of residues relative to the reference position, whereby the sequence of the portion is a contiguous sequence of nucleotides in the specified polynucleotide that has a defined length and located in a specified polynucleotide according to a defined position.
  • modification of nucleotides may mean that the nucleic acid described in the present invention is modified by methods mature in the art, such as “Current protocols innucleic acid chemistry” Beaucage, SL et al., (Edrs.), John Synthesis or modification is performed by methods described in Wiley & Sons, Inc., New York, NY, USA, which is hereby incorporated by reference.
  • the modification may include, but is not limited to: terminal modification, such as 5'-end modification (e.g., phosphorylation, conjugation, inverted linkage) or 3'-end modification (e.g., conjugation, DNA nucleotide , trans bond, etc.); base modification, such as replacement with stabilized bases, destabilized bases or bases paired with expanded pairing library bases, removal of bases (abasic nucleosides acid), or conjugated bases; sugar modifications (e.g., sugar modifications at the 2'-position or 4'-position) or substituted sugars; or backbone modifications, including phosphorus Acid diester bonds are modified or replaced.
  • terminal modification such as 5'-end modification (e.g., phosphorylation, conjugation, inverted linkage) or 3'-end modification (e.g., conjugation, DNA nucleotide , trans bond, etc.
  • base modification such as replacement with stabilized bases, destabilized bases or bases paired with expanded pairing library bases, removal of bases (abasic nucleoside
  • the term "substances that modify histones” usually refers to related enzymes that can modify histones and regulate gene transcription. Common modifications to histones can be methylation, acetylation, phosphorylation, etc. ionization, adenylation, ubiquitination, ADP ribosylation, etc.
  • methylation modification is used interchangeably with "DNA methylation” and "nucleic acid methylation”, which generally refers to making the gene fragments, nucleotides or bases thereof in this application have Methylation state, a process that often occurs inside cells that have been transfected with a nucleic acid containing a structural gene encoding a polypeptide operably linked to a promoter in which the promoter nucleic acid Cytosine is converted into 5-methylcytosine.
  • a promoter nucleic acid in which at least one cytosine is converted to 5-methylcytosine is called a "methylated" nucleic acid or DNA.
  • the DNA fragment in which the gene in this application is located may have methylation on one strand or multiple strands, or may have methylation on one site or multiple sites.
  • regulatory element refers to a genetic element capable of controlling the expression of a nucleic acid sequence.
  • splicing signals, promoter sequences, polyadenylation signals, transcription termination sequences, upstream regulatory domains, replication origins, internal ribosome entry sites ("IRES"), enhancers, etc. which together provide the coding sequence with the Replication, transcription, and translation in recipient cells. Not all of these control sequences need to be present.
  • Transcription control signals in eukaryotes often contain "promoter” and “enhancer” elements. Promoters and enhancers are composed of short arrays of DNA sequences. Promoters are regulatory elements that promote the initiation of transcription of operably linked coding regions.
  • Enhancers increase genetics by increasing the activity of the closest promoter located on the same DNA molecule. Regulatory elements for the rate of transcription, sequences that specifically interact with cellular proteins involved in transcription (Maniatis et al., Science 236:1237 (1987), incorporated herein by reference in its entirety). Promoter and enhancer elements have been isolated from a variety of eukaryotic sources, including genes in yeast, insect and mammalian cells, and viruses (similar control sequences, known as promoters, are also found in prokaryotes). The choice of specific promoters and enhancers depends on the recipient cell type.
  • eukaryotic promoters and enhancers have a broad host range, whereas others are functional within a restricted subset of cell types (for review, see, e.g., Voss et al., Trends Biochem. Sci., 11:287 (1986); and Maniatis et al. (supra), incorporated herein by reference in their entirety).
  • the SV40 early gene enhancer is active in a variety of cell types from many mammalian species and has been used to express proteins in a variety of mammalian cells (Dijkema et al., EMBO J. 4:761 (1985) , incorporated herein by reference in its entirety).
  • Promoter and enhancer elements derived from the human elongation factor 1-alpha gene (Uetsuki et al., J. Biol. Chem., 264:5791 (1989); Kim et al., Gene 91:217 (1990); and Mizushima and Nagata, Nucl. Acids. Res., 18:5322 (1990)), the long terminal repeat of Rous sarcoma virus (Gorman et al., Proc. Natl. Acad. Sci.
  • Promoters and enhancers may occur naturally alone or together.
  • reverse The viral long terminal repeat contains promoter and enhancer elements.
  • promoters and enhancers act independently of the gene being transcribed or translated.
  • the enhancers and promoters used may be "endogenous,”"exogenous,” or “heterologous” relative to the gene to which they are operably linked.
  • An “endogenous” enhancer/promoter is one that is naturally associated with a given gene in the genome.
  • a “foreign” or “heterologous” enhancer or promoter is one that is juxtaposed with a gene through genetic manipulation (i.e., molecular biology techniques) such that transcription of the gene is enhanced by the connection Sub/Promoter Guidance.
  • the presence of a "splicing signal" on an expression vector usually results in high-level expression of the recombinant transcript.
  • a “splicing signal” mediates removal of introns from the primary RNA transcript and consists of splice donor and acceptor sites (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, New York (1989), pp. 16.7-16.8, incorporated herein by reference in its entirety).
  • splice donor and acceptor sites are the splice junctions of the 16S RNA from SV40.
  • a "transcription termination signal” typically exists downstream of the polyadenylation signal and is hundreds of nucleotides in length.
  • the term "poly A signal” or “poly A sequence” refers to a DNA sequence that directs the termination and polyadenylation of nascent RNA transcripts. Efficient polyadenylation of recombinant transcripts is often necessary because transcripts lacking poly A signals are unstable and rapidly degraded.
  • the poly A signal used in the expression vector can be "heterologous” or "endogenous.”
  • the endogenous poly A signal is a signal naturally present at the 3' end of the coding region of a given gene in the genome.
  • a heterologous poly A signal is one that is isolated from one gene and operably linked to the 3' end of another gene.
  • a commonly used heterologous poly A signal is the SV40 poly A signal.
  • the SV40 poly A signal is contained on a 237 bp BamHI/BclI restriction fragment and directs termination and polyadenylation (Sambrook et al., supra, 16.6-16.7, incorporated by reference in its entirety).
  • DNA methyltransferase generally refers to an enzyme that catalyzes the transfer of methyl groups to DNA.
  • Non-limiting examples of DNA methyltransferases include DNMT1, DNMT 3A, DNMT 3B, and DNMT 3L.
  • DNA methyltransferases can modify the activity of DNA fragments (such as regulating gene expression) without changing the DNA sequence.
  • gene expression regulatory molecules may include one or more (eg, two) DNA methyltransferases.
  • the DNA methyltransferase domain comprises at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, 90 A variant of the amino acid sequence that has %, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% sequence identity, or homologues.
  • the DNA methyltransferase domain comprises at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least Amino acids with 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% sequence identity Sequence variants or homologs.
  • the term "functionally active fragment” generally refers to a fragment that has a partial region of a full-length protein or nucleic acid, but retains or partially retains the biological activity or function of the full-length protein or nucleic acid.
  • a functionally active fragment may retain or partially retain the ability of the full-length protein to bind another molecule.
  • a functionally active fragment of a DNA methyltransferase may retain or partially retain the biologically active function of a full-length DNA methyltransferase to catalyze the transfer of methyl groups to DNA.
  • direct and/or indirect connection generally refer to the opposite “direct connection” or “indirect connection”.
  • the term “directly connected” generally means directly connected or directly coupled.
  • the direct connection can be a situation where the connected substances (such as amino acid sequence segments) are directly connected without spacing components (such as amino acid residues or derivatives thereof); for example, the amino acid sequence segment X and another amino acid sequence Segment Y is directly connected through an amide bond formed by the C-terminal amino acid of amino acid sequence segment X and the N-terminal amino acid of amino acid sequence segment Y.
  • “Indirect connection” usually refers to a situation where the connected substances (such as amino acid sequence segments) are indirectly connected by a spacer component (such as an amino acid residue or its derivative).
  • the term “Krab” is also referred to as "Krüppel-related box domain” or “Krüppel-related box domain”, which generally refers to the transcriptional repression domain present in transcription factors of human zinc finger proteins. About 45 to about 75 amino acid residues.
  • the Krab domain may comprise at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% amino acid sequence identity Sequence variants or homologues.
  • delivery vector generally refers to a transfer vehicle capable of delivering an agent (eg, a nucleic acid molecule) to a target cell.
  • Delivery vehicles can deliver agents to specific cell subtypes. For example, by means of inherent characteristics of the delivery vehicle or by means of a moiety coupled to, contained within (or a moiety bound to the carrier) such that the moiety and the delivery vehicle are maintained together, thereby rendering the moiety sufficient to target the target.
  • the delivery vehicle may also increase the in vivo half-life of the agent to be delivered and/or the bioavailability of the agent to be delivered.
  • Delivery vectors may include viral vectors, virus-like particles, polycationic vectors, peptide vectors, liposomes, and/or hybrid vectors.
  • the properties of the delivery vehicle e.g., size, charge, and/or pH
  • the properties of the delivery vehicle can effectively deliver the delivery vehicle and/or molecules entrapped therein to the target cells, reduce immune clearance and/or promote retention in the target cell.
  • the term "liposome” generally refers to a vesicle having an internal space separated from an external medium by a membrane of one or more bilayers.
  • the membrane of the bilayer may be formed by amphipathic molecules, such as synthetic or naturally derived lipids containing spatially separated hydrophilic and hydrophobic domains; in other embodiments, the bilayer
  • the film of layers can be formed by amphiphilic polymers and surfactants.
  • the liposomes are spherical vesicular structures composed of a single or multilamellar lipid bilayer surrounding an internal aqueous compartment, and a relatively impermeable outer lipophilic phospholipid bilayer. consists of sub-layers.
  • liposomes are biocompatible, nontoxic, can deliver hydrophilic and lipophilic drug molecules, protect their cargo from degradation by plasma enzymes, and transport their cargo across biological membranes and the blood-brain barrier (BBB).
  • BBB blood-brain barrier
  • Liposomes can be made from several different types of lipids such as phospholipids. Liposomes may contain natural phospholipids and lipids such as 1,2-distearoyl-sn-glycero-3-phosphatidylcholine (DSPC), sphingomyelin, lecithin, monosialoganglioside lipids or any combination thereof.
  • DSPC 1,2-distearoyl-sn-glycero-3-phosphatidylcholine
  • sphingomyelin sphingomyelin
  • lecithin monosialoganglioside lipids or any combination thereof.
  • monosialoganglioside lipids monosialogangli
  • the liposomes can also contain cholesterol, sphingomyelin and/or 1,2-dioleoyl - sn-glycero-3-phosphoethanolamine (DOPE), for example, to increase stability and/or prevent leakage of cargo within liposomes.
  • DOPE 1,2-dioleoyl - sn-glycero-3-phosphoethanolamine
  • lipid nanoparticle generally refers to particles containing multiple (ie, more than one) lipid molecules physically bound to each other (eg, covalently or non-covalently) by intermolecular forces.
  • LNPs can be, for example, microspheres (including unilamellar and multilamellar vesicles, such as liposomes), dispersed phase in emulsions, micelles or internal phase in suspensions.
  • LNPs can encapsulate nucleic acids within cationic lipid particles (eg, liposomes) and can be delivered to cells relatively easily. In some instances, lipid nanoparticles do not contain any viral components, which helps minimize safety and immunogenicity issues.
  • the lipid particles can be used for in vitro, ex vivo and in vivo delivery.
  • the lipid particles can also be used with cell populations of various sizes.
  • the LNPs of the present application can be readily prepared by various methods known in the art, such as by mixing an organic phase with an aqueous phase. Mixing of the two phases can be achieved using microfluidic devices and impinging flow reactors. The more thoroughly the organic phase and the aqueous phase are mixed, the better the embedding rate and particle size distribution of the LNP obtained.
  • the particle size of LNP can be adjusted by changing the mixing speed of the organic phase and the aqueous phase. The faster the mixing speed, the smaller the particle size of the prepared LNP will be.
  • LNPs can be used to deliver DNA molecules (eg, molecules containing coding sequences for DNA binding proteins and/or sgRNA) and/or RNA molecules (eg, Cas, sgRNA's mRNA). In some cases, LNPs can be used to deliver Cas/gRNA RNP complexes.
  • DNA molecules eg, molecules containing coding sequences for DNA binding proteins and/or sgRNA
  • RNA molecules eg, Cas, sgRNA's mRNA.
  • LNPs can be used to deliver Cas/gRNA RNP complexes.
  • LNPs are used to deliver mRNA and gRNA (eg, an mRNA fusion molecule comprising DNMT3A-DNMT3L(3A-3L)-dCas9-KRAB and at least one sgRNA targeting a target gene).
  • mRNA and gRNA eg, an mRNA fusion molecule comprising DNMT3A-DNMT3L(3A-3L)-dCas9-KRAB and at least one sgRNA targeting a target gene.
  • the term "recombinant vector” generally refers to a nucleic acid molecule capable of transporting it and another nucleic acid to which it is linked.
  • a vector refers to a circular double-stranded DNA ring within which additional DNA segments can be ligated.
  • the vector may be linear.
  • a viral vector in which additional DNA segments can be ligated into the viral genome.
  • Certain vectors are capable of autonomous replication within the host cell into which they are introduced (eg, bacterial vectors with bacterial origins of replication and episomal mammalian vectors). Other vectors (eg, non-episomal mammalian vectors) can integrate into the host cell's genome upon introduction into the host cell, and thereby replicate together with the host genome.
  • adeno-associated virus (AAV) vector generally refers to a vector having functional or partially functional ITR sequences and a transgene.
  • ITR refers to inverted terminal repeats. ITR sequences can be derived from adeno-associated virus serotypes, including but not limited to AAV-1, AAV-2, AAV-3, AAV-4, AAV-5, AAV-6, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12 and AAV13, and any AAV variant or mixture.
  • the ITR need not be a wild-type nucleotide sequence, and may be altered (eg, by insertion, deletion, or substitution of nucleotides) as long as the sequence retains functions that provide functional rescue, replication, and packaging.
  • the AAV vector may have one or more AAV wild-type genes, preferably the rep and/or cap genes, deleted in whole or in part, but retaining functional flanking ITR sequences. Functional ITR sequences serve, for example, to rescue, replicate and package AAV virions or particles. Therefore, an "AAV vector" is defined in this application to include at least those sequences required for insertion of a transgene into cells of a subject. Optionally included are those cis-sequences necessary for viral replication and packaging (eg, functional ITR).
  • nuclear localization sequence or “nuclear localization signal” or “NLS” generally refers to a peptide that directs a protein to the nucleus.
  • NLS includes five basic positively charged amino acids.
  • NLS can be located anywhere on the peptide chain.
  • complementary generally refers to the ability of a nucleic acid to form hydrogen bonds with another nucleic acid sequence via traditional Watson-Crick or other non-traditional types.
  • sequence A-G-T is complementary to the sequence T-C-A.
  • Percent complementarity indicates the percentage of residues in a nucleic acid molecule that can form hydrogen bonds (e.g., Watson-Crick base pairing) with a second nucleic acid sequence (e.g., 50 out of 10, 6, 7, 8, 9, 10, respectively) %, 60%, 70%, 80%, 90% and 100% complementary).
  • perfect complementary means that all contiguous residues of a nucleic acid sequence will hydrogen bond to the same number of contiguous residues in a second nucleic acid sequence.
  • substantially complementary means that at 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, Within a region of 40, 45, 50 or more nucleotides, or refers to at least 60%, 65%, 70%, 75%, 80%, A degree of complementarity of 85%, 90%, 95%, 97%, 98%, 99% or 100%.
  • the term "gene” generally refers to a DNA segment designed to produce a protein.
  • the gene may also include regions before and after the coding region (leader and tail) as well as intervening sequences (introns) between individual coding segments (exons). Leaders, tails, and introns include regulatory elements necessary for gene transcription and translation.
  • a "protein gene product” may be a protein expressed by a specific gene.
  • polypeptide or amino acid residues.
  • a fusion protein may refer to a chimeric protein encoding two or more separate protein sequences recombinantly expressed as a single part.
  • identity refers to the use of the BLAST or BLAST 2.0 sequence comparison algorithm with the default parameters described below or by manual alignment and visual inspection. Measured by inspection.
  • identical or having a specified percentage of identical amino acid residues or nucleotides when comparing and aligning for maximum correspondence over a comparison window or specified region, approximately 60% identity within a specified region, preferably 65 %, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or higher consistency) of two or more Multiple sequences or subsequences, such sequences may be said to be "substantially identical".
  • guide RNA or "gRNA” generally refers to any polynucleotide sequence that has sufficient complementarity to a target polynucleotide sequence to hybridize to the target sequence and specifically bind the CRISPR complex to the target sequence.
  • the degree of complementarity between a guide sequence and its corresponding target sequence is about or greater than about 50%, about 60%, about 75%, about 80% when optimally aligned using a suitable alignment algorithm , about 85%, about 90%, about 95%, about 97.5%, about 99% or higher.
  • the specific protein may include any natural form of the protein or maintain the activity of the protein (for example, with at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% activity).
  • the variant or homolog has at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% Amino acid sequence identity.
  • linker is generally intended to include a linker that joins two or more moieties.
  • a linker is linked at the N-terminus and C-terminus to the amino acid sequence of the remainder of the compound (eg, a fusion protein provided herein).
  • XTEN XTEN linker
  • XTEN polypeptide refers to a recombinant polypeptide lacking hydrophobic amino acid residues.
  • detectable agent refers to a composition that can be detected by suitable means.
  • suitable means are, for example, spectroscopic, photochemical, biochemical, immunochemical, chemical, magnetic resonance imaging or other physical means.
  • useful detectable reagents include radioactive elements, fluorophores (eg, fluorescent dyes), electron-dense reagents, enzymes (eg, commonly used in ELISA), biotin, paramagnetic molecules, and the like.
  • the terms “inhibit”, “repress”, “silence” and the like generally refer to the reduction of gene expression and/or activity.
  • administration of a substance of the present application may negatively affect (e.g., decrease) the activity of a nucleic acid sequence relative to the activity of a nucleic acid sequence in the absence of the substance (e.g., fusion protein, complex, nucleic acid, vector) (control) .
  • suppression may refer to a reduction of a disease or symptoms of a disease.
  • inhibition includes at least partially, partially or completely blocking activation (eg, transcription) of a nucleic acid sequence, or reducing, preventing, or delaying activation of a nucleic acid sequence.
  • the inhibitory activity may be 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, or less of the control.
  • selected from is generally intended to include selected objects and all combinations thereof.
  • selected from (:)A, “B and C” is meant to include all combinations of A, B and C, for example, A, B, C, A+B, A+C, B+C or A+B+C.
  • the term "about” generally refers to a variation within the range of 0.5% to 10% above or below the specified value, such as 0.5%, 1%, 1.5%, 2%, 2.5%, above or below the specified value. 3%, 3.5%, 4%, 4.5%, 5%, 5.5%, 6%, 6.5%, 7%, 7.5%, 8%, 8.5%, 9%, 9.5%, or 10%.
  • the present application provides a method for regulating F11 gene expression and/or activity.
  • the method includes providing a gene expression regulating molecule or a nucleic acid encoding the gene expression regulating molecule.
  • the gene expression regulating molecule may have Modulate the expression of the F11 gene without changing the function of its gene sequence.
  • the methods of the present application may be non-therapeutic methods.
  • the method of the present application may not directly target the human body.
  • the methods of the present application may be in vitro or ex vivo methods.
  • the methods of the present application may be methods for therapeutic purposes.
  • the methods of the present application may be in vivo methods.
  • the present application provides a method for treating and/or alleviating conditions associated with abnormal F11 gene expression and/or F11 gene activity, the method comprising providing a gene expression regulatory molecule or encoding the gene expression regulator
  • the gene expression regulating molecule may have the function of regulating the expression of the F11 gene without changing its gene sequence.
  • the present application provides a gene expression regulatory molecule or a nucleic acid encoding the gene expression regulatory molecule.
  • the gene expression regulatory molecule may have the function of regulating the expression of the F11 gene without changing the gene sequence.
  • the nucleic acid includes DNA and/or mRNA.
  • the gene expression regulatory molecule or the nucleic acid encoding the gene expression regulatory molecule can be used to treat and/or alleviate conditions related to abnormal F11 gene expression and/or F11 gene activity.
  • the present application provides a gene expression regulatory molecule or a nucleic acid encoding the gene expression regulatory molecule in the preparation of a medicament for treating and/or alleviating conditions associated with abnormal F11 gene expression and/or F11 gene activity.
  • the gene expression regulating molecule may have the function of regulating the expression of the F11 gene without changing its gene sequence.
  • the nucleic acid encoding the gene expression regulatory molecule of the present application includes DNA and/or mRNA.
  • the present application provides a nucleic acid binding molecule or a nucleic acid encoding the nucleic acid binding molecule, the nucleic acid binding molecule comprising the sequence shown in any one of SEQ ID NOs: 1-70.
  • the nucleic acid encoding the nucleic acid binding molecule of the present application includes DNA and/or mRNA.
  • a recombinant vector comprising the nucleic acid of the present application.
  • a recombinant vector may refer to a nucleic acid molecule capable of transporting another nucleic acid to which it is linked.
  • Recombinant vectors may include single-stranded, double-stranded, or partially double-stranded nucleic acid molecules; nucleic acid molecules containing one or more free ends, without free ends (e.g., circular); nucleic acid molecules containing DNA, RNA, or both; and Other types of polynucleotides known in the art. For example, you can use the disease poison carrier.
  • Viral vectors may contain virus-derived DNA or RNA sequences for packaging into viruses (eg, retroviruses, replication-deficient retroviruses, adenoviruses, replication-deficient adenoviruses, and adeno-associated viruses (AAV)).
  • viruses eg, retroviruses, replication-deficient retroviruses, adenoviruses, replication-deficient adenoviruses, and adeno-associated viruses (AAV)).
  • viruses eg, retroviruses, replication-deficient retroviruses, adenoviruses, replication-deficient adenoviruses, and adeno-associated viruses (AAV)
  • viruses eg, retroviruses, replication-deficient retroviruses, adenoviruses, replication-deficient adenoviruses, and adeno-associated viruses (AAV)
  • viruses eg, retroviruses, replication-deficient retroviruses, aden
  • the present application provides a delivery vector, the delivery vector comprising the nucleic acid binding molecule of the present application, the gene expression regulatory molecule of the present application, the nucleic acid of the present application, and/or the recombinant vector of the present application, and optionally containing liposomes and/or lipid nanoparticles (LNP).
  • a delivery vector may comprise one or more Cas proteins and one or more guide RNAs, for example, in the form of a ribonucleoprotein complex (RNP).
  • RNP ribonucleoprotein complex
  • ribonucleoproteins can be delivered via polypeptide-based shuttle agents.
  • ribonucleoproteins can be delivered using synthetic peptides.
  • the delivery vector can be introduced into the cell by physical delivery methods.
  • physical methods include microinjection, electroporation, and hydrodynamic delivery.
  • LNPs can encapsulate nucleic acids in cationic lipid particles (such as liposomes) and can be delivered to cells relatively easily.
  • lipid nanoparticles do not contain any viral components, which helps minimize safety and immunogenicity concerns.
  • Lipid particles can be used for in vitro, ex vivo and in vivo delivery.
  • the components of the LNP may include cationic lipids, ionizable lipids, pegylated lipids and/or support lipids, and optionally a cholesterol component.
  • the LNP can comprise ionizable lipid (20%-70%, molar ratio), pegylated lipid (0%-30%, molar ratio), support lipid (30%-50% , molar ratio) and cholesterol (10%-50%, molar ratio).
  • the present application provides a composition comprising the nucleic acid binding molecule of the present application, the gene expression regulating molecule of the present application, the nucleic acid of the present application, the recombinant vector of the present application, and/or the present application. Delivery vehicle.
  • the nucleic acid binding molecule, the gene expression modulating molecule, the nucleic acid encoding the nucleic acid binding molecule, the nucleic acid encoding the gene expression modulating molecule, the recombinant vector and the delivery vector in the composition can be included in one composition at the same time, or separately. Contained in different compositions.
  • nucleic acid binding molecule when using a nucleic acid binding molecule, a gene expression regulating molecule, a nucleic acid encoding the nucleic acid binding molecule, a nucleic acid encoding the gene expression regulating molecule, a recombinant vector and/or a delivery vector in the composition, they can be used simultaneously, or Use separately.
  • the present application provides a cell comprising the nucleic acid binding molecule of the present application, the gene expression regulating molecule of the present application, the nucleic acid of the present application, the recombinant vector of the present application, the delivery vector of the present application, and/ or compositions of the present application.
  • the present application provides a kit, which includes the nucleic acid binding molecule of the present application, the gene expression regulating molecule of the present application, the nucleic acid of the present application, the recombinant vector of the present application, the delivery vector of the present application, The composition of the present application, and/or the cell of the present application.
  • the present application provides a method for regulating the expression and/or activity of a target gene, which method includes providing the nucleic acid binding molecule of the present application, the gene expression regulating molecule of the present application, the nucleic acid of the present application, and the recombinant of the present application. carrier, book The application's delivery vector, the application's composition, the application's cell, and/or the application's kit.
  • the methods can reduce the expression and/or activity of a gene of interest.
  • administration of a substance of the present application may negatively affect (e.g., reduce) the activity of a nucleic acid sequence compared to the expression and/or activity of a target gene in the absence of the substance of the present application, for example, may include at least partially, partially Block activation (e.g., transcription) of a nucleic acid sequence completely or completely, or reduce, prevent, or delay activation of a nucleic acid sequence.
  • the inhibitory activity can be about 90%, about 80%, about 70%, about 60%, about 50%, about 40%, about 30%, about 20%, about 10%, or less of the control.
  • the present application provides a nucleic acid binding molecule of the present application, a gene expression regulating molecule of the present application, a nucleic acid of the present application, a recombinant vector of the present application, a delivery vector of the present application, a composition of the present application, and a nucleic acid binding molecule of the present application.
  • the application of the cells and/or the kit of the present application in the preparation of medicaments for treating and/or alleviating disorders, including disorders associated with abnormal expression and/or activity of target genes.
  • the present application provides a nucleic acid binding molecule of the present application, a gene expression regulating molecule of the present application, a nucleic acid of the present application, a recombinant vector of the present application, a delivery vector of the present application, a composition of the present application, and a nucleic acid binding molecule of the present application.
  • the cells, and/or the kits of the present application are used to treat and/or alleviate disorders, including disorders associated with abnormal expression and/or activity of target genes.
  • the present application provides a method for treating and/or alleviating diseases, which method includes providing the nucleic acid binding molecule of the present application, the gene expression regulating molecule of the present application, the nucleic acid of the present application, the recombinant vector of the present application, In the delivery vector of the present application, the composition of the present application, the cells of the present application, and/or the kit of the present application, the disease includes a disease related to abnormal expression and/or activity of the target gene.
  • the treatment is a disease/disorder of the organ, illustratively including liver disease, eye disease, muscle disease, heart disease, blood disease, encephalopathy, kidney disease, or may include treatment of autoimmune disease, central nervous system disease , cancer and other proliferative diseases, neurodegenerative diseases, inflammatory diseases, metabolic diseases, musculoskeletal diseases, etc.
  • the gene expression molecules provided in the present application or the method of the present application have the function of regulating the expression of the F11 gene without changing its gene sequence.
  • the gene expression regulatory molecule may have the function of inhibiting gene expression.
  • the gene expression modulating molecule comprises a DNA binding domain.
  • the gene expression regulatory molecule may have the function of binding to a gene sequence.
  • the DNA binding domain includes a (DNA) nuclease, and the nuclease can be a nuclease that targets DNA in a sequence-specific manner; exemplarily, it can be a CRISPR-Cas system-related enzyme, a zinc finger nuclease ( ZFN), transcription activator-like effector nucleases (TALENs) or meganucleases.
  • the gene expression regulatory molecule may comprise the DNA binding domain of a TALEN, a zinc finger domain, and/or the DNA binding domain of a CRISPR/Cas system.
  • the DNA binding domain is a DNA nuclease derived from the CRISPR-Cas system.
  • the DNA-binding domain is a (modified) transcription activator-like effector nuclease (TALEN) system; while transcription activator-like effector (TALE) can be designed to bind almost any desired DNA sequence.
  • the DNA binding domain is or consists of a (modified) zinc finger nuclease (ZFN) system; the ZFN system uses an artificial protein generated by fusing a zinc finger DNA binding domain to a DNA cleavage domain. Restriction enzymes, DNA-cutting domains that can be engineered to target a desired DNA sequence.
  • the DNA binding domain is a (modified) meganuclease, which is an endodeoxyribonuclease characterized by a large recognition site (double-stranded DNA sequence of 12 to 40 base pairs) .
  • the gene expression regulatory molecule may comprise a Cas enzyme.
  • the gene expression modulating molecule may comprise a Cas enzyme that has substantially no nuclease activity.
  • a guide sequence can be any polynucleotide sequence that has sufficient complementarity to a target polynucleotide sequence to hybridize to the target sequence and direct sequence-specific binding of the CRISPR complex to the target sequence.
  • a nucleic acid-targeting Cas protein can be mutated relative to the corresponding wild-type enzyme such that the mutated nucleic acid-targeting Cas protein lacks the ability to cleave one or both strands of a target polynucleotide.
  • the DNA cleavage activity of a mutant enzyme is about 25%, 10%, 5%, 1%, 0.1%, 0.01%, or less of the nucleic acid cleavage activity of a non-mutated form of the enzyme.
  • a mutated Cas can have one or more mutations that result in reduced off-target effects.
  • the gene expression regulatory molecule may comprise a Cas9 enzyme.
  • Cas proteins include Class I (eg, Types I, III, and IV) and Class 2 (eg, Type II, V, and VI) Cas proteins, such as Cas9, Cas12 (eg, Cas12a, Cas12b, Cas12c, Cas12d), Cas13 (e.g., Cas13a, Cas13b, Cas13c, Cas13d), CasX, CasY, Cas14, variants thereof (e.g., mutated forms, truncated forms), their homologs, and their orthologs.
  • Cas proteins include Class I (eg, Types I, III, and IV) and Class 2 (eg, Type II, V, and VI) Cas proteins, such as Cas9, Cas12 (eg, Cas12a, Cas12b, Cas12c, Cas12d), Cas13 (e.g., Cas13a, Cas13b, Ca
  • the Cas protein is Cas9, Cas12a, Cas12b, Cas12c, or Cas12d.
  • Cas9 can be SpCas9, SaCas9, StCas9, and other Cas9 orthologs.
  • Cas12 can be Cas12a, Cas12b and Cas12c, including FnCas12a, or homologs or orthologs thereof.
  • the Cas9 enzyme can include Staphylococcus aureus dCas9, Streptococcus pyogenes dCas9, Campylobacter jejuni dCas9, Corynebacterium diphtheria dCas9, Eubacterium ventriosum dCas9, Streptococcus pasteurianus dCas9, Lactobacillus farciminis dCas9, Sphaerochaeta globus dCas9, Azospirillum ( For example, B510)dCas9, Gluconacetobacter diazotrophicus dCas9, Neisseria cinerea dCas9, Roseburia intestinalis dCas9, Parvibaculum lavamentivorans dCas9, Nitratifractor salsuginis (eg, DSM 16511) dCas9, Campylo
  • the gene expression regulatory molecule may comprise the amino acid sequence of dCas9.
  • the dCas9 sequence may have one, two, three, four, five or more changes, such as amino acid substitutions, insertions or deletions of the sequence, or any fragment thereof.
  • the gene expression regulatory molecule is capable of binding to a DNA region or a fragment thereof within 500 bp upstream and/or downstream of the transcription start site (TSS) of the F11 gene.
  • TSS transcription start site
  • the gene expression regulatory molecule can bind to about 100bp, about 200bp, about 300bp, about 400bp, about 500bp, about 600bp, about 700bp, about 800bp, about 900bp, about 1000bp, about 1100bp, about 1200bp upstream of the TSS , about 1300bp, about 1400bp or about 1500bp.
  • the gene expression regulatory molecule can bind to about 100bp, about 200bp, about 300bp, about 400bp, about 500bp, about 600bp, about 700bp, about 800bp, about 900bp, about 1000bp, about 1100bp, about 1200bp downstream of the TSS , about 1300bp, about 1400bp or about 1500bp.
  • the gene expression regulatory molecule can bind to the DNA region or fragments thereof located in any one of SEQ ID NOs: 71-72.
  • the gene expression regulatory molecule can bind to one or more DNA regions near the transcription start site (TSS) of the F11 gene described below: between 250 bp upstream of the TSS and 130 bp upstream. between 50bp upstream and 120bp downstream of TSS, and between 230bp downstream and 390bp downstream of TSS.
  • TSS transcription start site
  • the gene expression regulatory molecule is capable of binding to one or more DNA regions near the transcription start site (TSS) of the F11 gene: between 250 bp upstream and 230 bp upstream of the TSS (e.g., Between 248-229 bp upstream of TSS), between 210 bp upstream of TSS and 180 bp upstream (for example, between 202-185 bp upstream of TSS), between 160 bp upstream of TSS and 130 bp upstream (for example, 156-137 bp upstream of TSS between), between 50 bp upstream of TSS and 10 bp downstream (for example, between 44-25 bp upstream of TSS, and/or between 12 bp upstream and 8 bp downstream), between 30 bp downstream of TSS and 60 bp downstream (for example, between TSS Between 37-56 bp downstream of TSS), between 90 bp downstream of TSS and 120 bp downstream (for example, between 96-115 bp
  • TSS
  • the gene expression modulating molecule comprises a first functional domain that provides modification of at least one nucleotide near the F11 gene and/or within the F11 gene regulatory element.
  • the first functional domain can regulate target gene expression through epigenetic modification at a regulatory element of the target gene, such as a promoter, enhancer, or transcription start site, such as through histone acetylation or Methylation, or DNA methylation.
  • regulatory elements may include a transcription start site, a core promoter, a proximal promoter, a distal enhancer, a silencer, an insulator element, a boundary element, or a locus control region.
  • the epigenetic modification can be through any known epigenetic modification modulator that can be used for DNA methylation.
  • exemplary epigenetic modification modulators can include DNA methyltransferases (e.g., DNMT3A or DNMT3A-DNMT3L), DNA demethylases (e.g., TET1 catalytic domain or TDG) and/or functionally active fragments thereof.
  • the first functional domain may provide modification of at least one nucleotide near the F11 gene and/or within the regulatory element of the F11 gene, and the modification of the at least one nucleotide includes a methylation modification.
  • the first functional domain comprises an epigenetic modification modulator, which may have DNA methylase activity.
  • the epigenetic modification modulator may have methylase activity, which involves the transfer of methyl groups to DNA, RNA, proteins, small molecules, cytosine, or adenine.
  • the modification can be located about 100 bp, about 200 bp, about 300 bp, about 400 bp, about 500 bp, about 600 bp, about 700 bp, about 800 bp, about 900 bp, about 1000 bp, about 1100 bp, about 1200 bp upstream of the transcription start site of the target gene. , about 1300bp, about 1400bp or about 1500bp.
  • the modification can be located about 100 bp, about 200 bp, about 300 bp, about 400 bp, about 500 bp, about 600 bp, about 700 bp, about 800 bp, about 900 bp, about 1000 bp, about 1100 bp, about 1200 bp downstream of the transcription start site of the target gene. , about 1300bp, about 1400bp or about 1500bp.
  • the first functional domain may comprise a DNA methyltransferase (DNMT) domain.
  • the first functional domain may comprise a DNMT 3A domain and/or a DNMT 3L domain.
  • the DNMT 3A domain and/or DNMT 3L domain is derived from mammals.
  • the DNMT 3A domain is derived from mice.
  • the gene expression regulatory molecule may comprise the amino acid sequence described in DNMT 3A.
  • the DNMT 3L domain is derived from human and/or mouse.
  • the gene expression regulatory molecule may comprise the amino acid sequence of DNMT 3L.
  • the sequence may have one, two, three, four, five or more changes relative to the above sequence, such as amino acid substitutions, insertions or deletions, or any fragment thereof.
  • the DNMT 3A domain and the DNMT 3L domain are directly and/or indirectly connected.
  • the DNMT 3A domain and the DNMT 3L domain are connected through a linker.
  • the C-terminal of the DNMT 3A structural domain is connected to the N-terminal of the DNMT 3L, or the C-terminal of the DNMT 3L structural domain is connected to the N-terminal of the DNMT 3A.
  • the gene expression modulating molecule comprises a second functional domain comprising a zinc finger protein-based transcription factor or a functionally active fragment thereof, or a substance capable of modifying histones.
  • the second functional domain may include a gene expression repressor, which may be any known gene expression repressor.
  • Exemplary gene expression repressors may be selected from the group consisting of Krüppel-related box (KRAB) domains, mSin3 interaction structures domain (SID), MAX interacting protein 1 (MXI1), chromosome shadow domain, EAR-repressor domain (SRDX), eukaryotic release factor 1 (ERF1), eukaryotic release factor 3 (ERF3), tetracycline repressor, lad repressor, Catharanthus roseus G-box binding factors 1 and 2, Drosophila Groucho (Drosophila Gro protein), tripartite motif-containing 28 (TRTM28), nuclear receptor corepressor 1, nuclear receptor corepressor 2, or functionally active fragments or fusions thereof.
  • KRAB Krüppel-related box
  • SID mSin3 interaction structures domain
  • MXI1 MAX interacting protein 1
  • chromosome shadow domain chromosome shadow domain
  • SRDX EAR-repressor domain
  • EEF1
  • the second functional domain may comprise a substance capable of modifying histones. qualitative function.
  • the second functional domain can comprise a Krab domain.
  • the second functional domain may comprise a ZIM3 Krab domain or a KOX1 Krab domain.
  • the KRAB domain or fragment thereof can be fused to the C-terminus of the dCas9 molecule. In certain embodiments, the KRAB domain or fragment thereof can be fused to the N-terminus and C-terminus of the dCas9 molecule.
  • the second functional domain may comprise a KRAB domain that may comprise substantially the same (e.g., at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or greater identity), or identical to ZIM3 Krab or KOX1 Krab , a sequence with two, three, four, five or more changes (e.g., amino acid substitutions, insertions, or deletions relative to ZIM3 Krab or KOX1 Krab), or any fragment thereof.
  • a KRAB domain may comprise substantially the same (e.g., at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or greater identity), or identical to ZIM3 Krab or KOX1 Krab ,
  • the second functional domain may include a gene expression activator, which may be any known gene expression activator.
  • exemplary gene expression activators may include VP16 activation domain, VP64 activation domain, p65 activation domain. Domain, Epstein-Barr virus R transactivator Rta molecule or fragment thereof.
  • the second functional domain may comprise a substance capable of modifying histones, which may comprise a histone acetyltransferase (e.g., p300 catalytic domain), a histone deacetylase, Histone methyltransferases (eg, SUV39H1 or G9a (EHMT2)), histone demethylases (eg, LSD1), and/or functionally active fragments thereof.
  • histone acetyltransferase e.g., p300 catalytic domain
  • a histone deacetylase eg, Histone methyltransferases (eg, SUV39H1 or G9a (EHMT2)
  • histone demethylases eg, LSD1
  • the gene expression regulatory molecule includes the first functional domain and the second functional domain, and the first functional domain is directly or indirectly connected to one end of the second functional domain. , or the first functional domain is directly and/or indirectly connected to both ends of the second functional domain.
  • the C-terminal of the first functional domain is directly connected to the N-terminal of the second functional domain, or the C-terminal of the first functional domain is indirectly connected (for example, through a linker) to the N-terminal of the second functional domain.
  • the N-terminus, or the first functional domain is located on the N-terminal side of the second functional domain (for example, from the N-terminus to the C-terminus, the first functional domain, other parts such as the DNA binding domain, and the order of two functional domains).
  • the C-terminal of the second functional domain is directly connected to the N-terminal of the first functional domain, or the C-terminal of the second functional domain is indirectly connected (for example, through a linker) to the N-terminal of the first functional domain.
  • the N-terminus, or the second functional domain is located on the N-terminal side of the first functional domain (for example, from the N-terminus to the C-terminus, there may be the second functional domain, other parts such as the DNA-binding domain, and the a sequence of functional domains).
  • the first functional domain includes two or more functional domains, and they can be directly connected, indirectly connected (for example, through a linker), or located on the N-terminal side of the second functional domain.
  • first functional domain a other parts such as the DNA-binding domain, the second functional domain, and the first functional domain b, or the first functional domain
  • the first functional domain and the second functional domain are directly or indirectly linked to one end of the DNA binding domain.
  • the first functional domain and the second functional domain are directly or indirectly connected to the C-terminus of the DNA binding domain.
  • the gene regulatory molecule may include dCas9-DNMT 3A-DNMT 3L-Krab , dCas9-DNMT 3L-DNMT 3A-Krab, dCas9-Krab-DNMT 3A-DNMT 3L, dCas9-Krab-DNMT 3L-DNMT 3A.
  • the first functional domain and the second functional domain are directly or indirectly connected to the N-terminus of the DNA binding domain.
  • the gene regulatory molecule may include DNMT 3A-DNMT 3L-Krab-dCas9 , DNMT 3L-DNMT 3A-Krab-dCas9, Krab-DNMT 3A-DNMT 3L-dCas9, Krab-DNMT 3L-DNMT 3A-dCas9.
  • the first functional domain and the second functional domain are directly or indirectly connected at both ends of the DNA binding domain.
  • the first functional domain is directly or indirectly connected to the C-terminal of the DNA-binding domain
  • the second functional domain is directly or indirectly connected to the N-terminal of the DNA-binding domain.
  • the The gene regulatory molecule may include any one of Krab-dCas9-DNMT 3A-DNMT 3L and Krab-dCas9-DNMT 3L DNMT 3A.
  • the first functional domain is directly or indirectly connected to the N-terminal of the DNA-binding domain
  • the second functional domain is directly or indirectly connected to the C-terminal of the DNA-binding domain.
  • the The gene regulatory molecule may include any one of DNMT 3A-DNMT 3L-dCas9-Krab and DNMT 3L-DNMT 3A-dCas9-Krab.
  • the gene expression modulating molecule may further comprise a tag for detection, isolation and/or purification.
  • the gene expression regulatory molecule can include an HA tag.
  • the gene expression regulatory molecule may comprise the amino acid sequence of an HA tag. Alternatively, a sequence having one, two, three, four, five or more changes relative to the above sequence, such as amino acid substitutions, insertions or deletions, or any fragment thereof.
  • the gene expression modulating molecule may further comprise a nuclear localization sequence.
  • the nuclear localization sequence may comprise amino acids with electropositive groups.
  • the nuclear localization sequence may comprise the amino acid sequence of a nuclear localization sequence known in the art.
  • the sequence may have one, two, three, four, five or more changes relative to the above sequence, such as amino acid substitutions, insertions or deletions, or any fragment thereof.
  • the nuclear localization sequence may be located at the N-terminus and/or C-terminus of the first functional domain, the N-terminus and/or C-terminus of the second functional domain, and/or the N-terminus of the DNA binding domain. and/or C-terminal.
  • the gene expression modulating molecule may further comprise a detectable moiety.
  • the detectable moiety may comprise blue fluorescent protein and/or green fluorescent protein.
  • the detectable moiety and the first functional domain, the second functional domain, the DNA binding domain, and/or the nuclear localization sequence can be linked by a self-cleaving peptide.
  • the self-cleaving peptide may comprise 2A peptide.
  • the first functional domain, the second functional domain, the DNA binding domain and other elements included in the gene regulatory molecule can be connected in an indirect manner, for example, through a certain length of Adapter sequence ligation.
  • the linker may include approximately 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 60, 70, 80, 90, 100 or more amino acids.
  • the first functional domain and the second functional domain are connected by a linker of about 80 or more amino acids in length.
  • the first functional domain and the second functional domain are connected by a linker of about 92 or more amino acids in length.
  • the first functional domain and the second functional domain are connected through an XTEN linker.
  • the linker comprises the amino acid sequence of an XTEN linker.
  • the linker comprises the amino acid sequence of an XTEN linker.
  • the linker includes an XTEN linker that is 16 amino acids in length, an XTEN linker that is 80 amino acids in length, or an amino acid sequence of a longer XTEN linker.
  • the present application also provides a nucleic acid binding molecule, which may comprise the sequence of any one of SEQ ID NOs: 1-70.
  • the nucleic acid binding molecules and/or the gene expression modulating molecules of the present application can be delivered to the subject by local injection, systemic infusion, or a combination thereof.
  • the nucleic acid binding molecule can comprise at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75% the sequence of any one of SEQ ID NOs: 1-70 , at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100 % sequence identity of the sequence.
  • the combination of the nucleic acid binding molecule and the gene expression modulating molecule of the present application may have the ability to modulate the expression level of the F11 gene.
  • the nucleic acid binding molecule and/or the gene expression regulating molecule of the present application can bind to the core promoter, proximal promoter, distal enhancer, silencer, insulator element, boundary element and/or locus control of the F11 gene district.
  • the nucleic acid binding molecule and/or the gene expression regulating molecule of the present application can bind to the DNA region within 500 bp upstream and/or downstream of the transcription start site of the F11 gene or a fragment thereof.
  • the nucleic acid binding molecule and/or the gene expression regulating molecule of the present application can bind to the DNA region or fragment thereof located in any one of SEQ ID NOs: 71-72.
  • the DNA region that can be combined can comprise at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75% of the DNA region in any one of SEQ ID NOs: 71-72. %, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or Sequences with 100% sequence identity.
  • the nucleic acid binding molecule and/or the gene expression regulating molecule of the present application can bind to the DNA region located in any one of SEQ ID NOs: 73-142 or a fragment thereof.
  • the DNA region that can be combined can comprise at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75% of the DNA region in any one of SEQ ID NOs: 73-142. %, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, to Sequences that are less than 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identical.
  • targeting any 20 bp region in the DNA region where any one of SEQ ID NOs: 73-142 is located can have the ability to regulate the expression level of the F11 gene.
  • administration of a substance of the present application may negatively affect (e.g., reduce) the activity of a nucleic acid sequence compared to target gene expression and/or activity in the absence of the substance of the present application, for example, may include at least partially, partially Either completely blocking the activation (eg, transcription) of the nucleic acid sequence, or reducing, preventing or delaying the activation of the nucleic acid sequence.
  • the inhibitory activity can be about 90%, about 80%, about 70%, about 60%, about 50%, about 40%, about 30%, about 20%, about 10%, or less of the control.
  • the guide sequence or spacer of the nucleic acid binding molecule can be 15 to 50 nucleotides in length.
  • the nucleic acid binding molecule is a guide RNA (gRNA), and the guide RNA can have a spacer length of at least 15 nucleotides.
  • the spacer length can be 15 to 17 nucleotides in length, 17 to 20 nucleotides in length, 20 to 24 nucleotides in length, 23 to 25 nucleotides in length. length, 24 to 27 nucleotides in length, 27 to 30 nucleotides in length, 30 to 35 nucleotides in length, or greater than 35 nucleotides in length.
  • the number of gRNAs administered can be at least 1 gRNA, at least 2 different gRNAs, at least 3 different gRNAs, at least 4 different gRNAs, at least 5 different gRNAs.
  • the target binding region can be between about 19 and about 21 nucleotides in length. In one embodiment, the target binding region may be 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides in length. In one embodiment, the target binding region may be complementary, eg, completely complementary, to the target region in the target gene. In one embodiment, the target binding region can be substantially complementary to the target region in the target gene.
  • the target binding region may comprise no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 regions that are different from the target region in the target gene.
  • complementary nucleotides in some embodiments, the nucleic acid binding molecules and/or gene expression modulating molecules of the present application can be formulated in liposomes or lipid nanoparticles. In some embodiments, the nucleic acid binding molecules and/or gene expression modulating molecules of the present application can be formulated in viral vectors.
  • a guide RNA can be included with one or more chemical modifications (e.g., by chemically linking two ribonucleotides or by replacing one or more ribonucleotides with one or more deoxyribonucleotides) of RNA-based molecules.
  • a target binding region of human origin can be targeted.
  • the DNA sequence of the reporter system in this example (standard font: promoter region, bold: F11 gene regulatory region, italics: green fluorescent protein (EGFP) sequence) is as follows:
  • DNA sequence of the editing tool EpiRegA (Dnmt3a-Dnmt3l-dCas9-KOX1 KRAB) (italic/underline italic: Dnmt3a/Dnmt3l, bold: dCas9, bold italic: KRAB, underline bold italic: blue fluorescent protein, standard font: junction sequence )as follows:
  • DNA sequence of the editing tool EpiRegB (Dnmt3a-Dnmt3l-ZIM3 KRAB-dCas9) (italic/underline italic: Dnmt3a/Dnmt3l, bold: dCas9, bold italic: KRAB, underline bold italic: blue fluorescent protein, standard font: junction sequence )as follows:
  • Amino acid sequence of editing tool EpiRegB (Dnmt3a-Dnmt3l-ZIM3 KRAB-dCas9) (italic/underline italic: Dnmt3a/Dnmt3l, bold: dCas9, bold italic: KRAB, underline bold italic: blue fluorescent protein, standard font: connection sequence , *: any amino acid) as follows:
  • DNA sequence of editing tool EpiRegC (dCas9-ZIM3 KRAB-DNMT3L-Dnmt3a) (italic/underline italic: Dnmt3a/Dnmt3l, bold: dCas9, bold italic: KRAB, underline bold italic: blue fluorescent protein, standard font: connection sequence )as follows:
  • Amino acid sequence of editing tool EpiRegC (dCas9-ZIM3 KRAB-DNMT3L-Dnmt3a) (italic/underline italic: Dnmt3a/Dnmt3l, bold: dCas9, bold italic: KRAB, underline bold italic: blue fluorescent protein, standard font: connection sequence , *: any amino acid) as follows:
  • Regional NT gRNA SEQ ID NO: 154) sample set to obtain the relative regulatory efficiency of different editing tools when using different gRNA.
  • SEQ ID NOs: 22, 23, 24, 26, 34, 35, 38, 45, 50 and 62 (their targeting regions 5' ends respectively start upstream of TSS
  • the gRNA shown in (44bp, upstream 248bp, downstream 37bp, downstream 96bp, upstream 12bp, upstream 156bp, downstream 233bp, upstream 204bp, downstream 301bp and downstream 366bp) combined with the epigenetic editing tool of this embodiment can effectively inhibit the expression of the F11 gene level.
  • the guide RNA in the epigenetic editing tool to target the target gene; at the same time, according to the gene expression regulatory molecules provided by this application, construct the table Epigenetic editing tools.
  • the region within 500 bp upstream and downstream of the F11 transcription start site (TSS) can be targeted.
  • the guide RNA plasmid and the gene expression regulatory molecule plasmid were co-transfected into mouse cell lines. After 72 hours, the top 10% of GFP+ and mCherry+ cells were sorted by FACS. RT-QPCR experiments were performed to evaluate the mRNA expression levels of target genes.
  • transfected cells showed reduced expression of the F11 expression product.
  • transfected cells may show reduced mRNA expression of F11 transcripts.
  • transfected cells may show reduced expression of the protein product of F11 expression.
  • diseases or conditions related to the F11 gene can be alleviated.
  • the epigenetic editing tool of the present application is used to regulate the expression of target points.
  • the domain in the gene expression regulating molecule that has the function of binding gene sequences can be replaced by the DNA-binding domain of TALEN, the zinc finger domain, the DNA-binding domain of tetR, a meganuclease and/or any CRISPR known in the art.
  • the nuclease domain of the Cas system such as dCas12 enzyme, etc.
  • the results show that the epigenetic target of the present application is versatile, and has a high effect of regulating gene expression using various gene sequence binding domains.

Abstract

L'invention concerne un procédé d'édition d'épigénome de cibles et son utilisation. En particulier, l'invention concerne un procédé de régulation du niveau d'expression d'un gène cible et d'une molécule de liaison à un acide nucléique. La combinaison de la molécule de liaison à l'acide nucléique et d'une molécule de régulation d'expression génique a la capacité de réguler le niveau d'expression du gène cible.
PCT/CN2023/112094 2022-08-11 2023-08-10 Procédé d'édition d'épigénome de cibles et son utilisation WO2024032678A1 (fr)

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