US20110202479A1 - Recognition sequences for i-crei-derived meganucleases and uses thereof - Google Patents

Recognition sequences for i-crei-derived meganucleases and uses thereof Download PDF

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US20110202479A1
US20110202479A1 US13/006,625 US201113006625A US2011202479A1 US 20110202479 A1 US20110202479 A1 US 20110202479A1 US 201113006625 A US201113006625 A US 201113006625A US 2011202479 A1 US2011202479 A1 US 2011202479A1
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meganuclease
crei
dna
sequence
cell
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Derek Jantz
James J. Smith
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Precision Biosciences Inc
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Precision Biosciences Inc
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Assigned to PRECISION BIOSCIENCES, INC. reassignment PRECISION BIOSCIENCES, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: JANTZ, DEREK, SMITH, JAMES J.
Publication of US20110202479A1 publication Critical patent/US20110202479A1/en
Priority to US14/315,676 priority patent/US9683257B2/en
Priority to US15/472,175 priority patent/US10273524B2/en
Priority to US15/472,168 priority patent/US10287626B2/en
Priority to US16/299,068 priority patent/US20190194729A1/en
Priority to US17/065,340 priority patent/US20210130874A1/en
Priority to US17/812,400 priority patent/US20230088311A1/en
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6811—Selection methods for production or design of target specific oligonucleotides or binding molecules
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N9/22—Ribonucleases RNAses, DNAses
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Definitions

  • the invention relates to the field of molecular biology and recombinant nucleic acid technology.
  • the invention relates to DNA sequences that can be recognized and cleaved by a non-naturally-occurring, rationally-designed, I-CreI-derived homing endonuclease and methods of using same.
  • the invention also relates to methods of producing recombinant nucleic acids, cells, and organisms using such meganucleases which cleave such DNA sites.
  • the invention further relates to methods of conducting a custom-designed, I-CreI-derived meganuclease business.
  • Genome engineering requires the ability to insert, delete, substitute and otherwise manipulate specific genetic sequences within a genome, and has numerous therapeutic and biotechnological applications.
  • the development of effective means for genome modification remains a major goal in gene therapy, agrotechnology, and synthetic biology (Porteus et al. (2005), Nat. Biotechnol. 23: 967-73; Tzfira et al. (2005), Trends Biotechnol. 23: 567-9; McDaniel et al. (2005), Curr. Opin. Biotechnol. 16: 476-83).
  • a common method for inserting or modifying a DNA sequence involves introducing a transgenic DNA sequence flanked by sequences homologous to the genomic target and selecting or screening for a successful homologous recombination event. Recombination with the transgenic DNA occurs rarely, but can be stimulated by a double-stranded break in the genomic DNA at the target site. Numerous methods have been employed to create DNA double-stranded breaks, including irradiation and chemical treatments. Although these methods efficiently stimulate recombination, the double-stranded breaks are randomly dispersed in the genome, which can be highly mutagenic and toxic. At present, the inability to target gene modifications to unique sites within a chromosomal background is a major impediment to successful genome engineering.
  • One approach to achieving this goal is stimulating homologous recombination at a double-stranded break in a target locus using a nuclease with specificity for a sequence that is sufficiently large to be present at only a single site within the genome (see, e.g., Porteus et al. (2005), Nat. Biotechnol. 23: 967-73).
  • the effectiveness of this strategy has been demonstrated in a variety of organisms using chimeric fusions between an engineered zinc finger DNA-binding domain and the non-specific nuclease domain of the FokI restriction enzyme (Porteus (2006), Mol Ther 13: 438-46; Wright et al. (2005), Plant J. 44: 693-705; Urnov et al.
  • a group of naturally-occurring nucleases which recognize 15-40 base-pair cleavage sites commonly found in the genomes of plants and fungi may provide a less toxic genome engineering alternative.
  • Such “meganucleases” or “homing endonucleases” are frequently associated with parasitic DNA elements, such as group 1 self-splicing introns and inteins. They naturally promote homologous recombination or gene insertion at specific locations in the host genome by producing a double-stranded break in the chromosome, which recruits the cellular DNA-repair machinery (Stoddard (2006), Q. Rev. Biophys. 38: 49-95).
  • LAGLIDADG Meganucleases are commonly grouped into four families: the LAGLIDADG family, the GIY-YIG family, the His-Cys box family and the HNH family. These families are characterized by structural motifs, which affect catalytic activity and recognition sequence. For instance, members of the LAGLIDADG family are characterized by having either one or two copies of the conserved LAGLIDADG motif (see Chevalier et al. (2001), Nucleic Acids Res. 29(18): 3757-3774). The LAGLIDADG meganucleases with a single copy of the LAGLIDADG motif form homodimers, whereas members with two copies of the LAGLIDADG motif are found as monomers.
  • I-CreI (SEQ ID NO: 1) is a member of the LAGLIDADG family which recognizes and cleaves a 22 base pair recognition sequence in the chloroplast chromosome, and which presents an attractive target for meganuclease redesign. Genetic selection techniques have been used to modify the wild-type I-CreI recognition site preference (Sussman et al. (2004), J. Mol. Biol. 342: 31-41; Chames et al. (2005), Nucleic Acids Res. 33: e178; Seligman et al. (2002), Nucleic Acids Res. 30: 3870-9, Arnould et al. (2006), J. Mol. Biol. 355: 443-58).
  • the DNA sequences recognized by I-CreI are 22 base pairs in length.
  • One example of a naturally-occurring I-CreI recognition site is provided in SEQ ID NO: 2 and SEQ ID NO: 3, but the enzyme will bind to a variety of related sequences with varying affinity.
  • the enzyme binds DNA as a homodimer in which each monomer makes direct contacts with a nine base pair “half-site” and the two half-sites are separated by four base pairs that are not directly contacted by the enzyme ( FIG. 1 a ).
  • I-CreI produces a staggered double-strand break at the center of its recognition sequences which results in the production of a four base pair 3′-overhang ( FIG.
  • the present invention concerns the central four base pairs in the I-CreI recognition sequences (i.e. the four base pairs that become the 3′ overhang following I-CreI cleavage, or “center sequence”, FIG. 1 b ).
  • this four base pair sequence is 5′-GTGA-3′.
  • the present invention is based, in part, upon the identification and characterization of a subset of DNA recognition sequences that can act as efficient substrates for cleavage by the rationally-designed, I-CreI-derived meganucleases (hereinafter, “I-CreI-derived meganucleases”).
  • the invention provides methods of identifying sets of 22 base pair DNA sequences which can be cleaved by I-CreI-derived meganucleases and which have, at their center, one of a limited set of four base pair DNA center sequences that contribute to more efficient cleavage by the I-CreI-derived meganucleases.
  • the invention also provides methods that use such DNA sequences to produce recombinant nucleic acids, cells and organisms by utilizing the recognition sequences as substrates for I-CreI-derived meganucleases, and products incorporating such DNA sequences.
  • the invention provides a method for cleaving a double-stranded DNA comprising: (a) identifying in the DNA at least one recognition site for a rationally-designed I CreI-derived meganuclease with altered specificity relative to I-CreI, wherein the recognition site is not cleaved by a naturally-occurring I-CreI, wherein the recognition site has a four base pair central sequence selected from the group consisting of TTGT, TTAT, TCTT, TCGT, TCAT, GTTT, GTCT, GGAT, GAGT, GAAT, ATGT, TTTC, TTCC, TGAC, TAAC, GTTC, ATAT, TCGA, TTAA, GGGC, ACGC, CCGC, CTGC, ACAA, ATAA, AAGA, ACGA, ATGA, AAAC, AGAC, ATCC, ACTC, ATTC, ACAT, GAAA, GGAA, GTCA, GTTA, GAAC, ATAT,
  • the invention provides a method for cleaving a double-stranded DNA comprising: (a) introducing into the DNA a recognition site for a rationally-designed I CreI derived meganuclease with altered specificity relative to I-CreI, wherein the recognition site is not cleaved by a naturally-occurring I-CreI, wherein the recognition site has a four base pair central sequence selected from the group consisting of TTGT, TTAT, TCTT, TCGT, TCAT, GTTT, GTCT, GGAT, GAGT, GAAT, ATGT, TTTC, TTCC, TGAC, TAAC, GTTC, ATAT, TCGA, TTAA, GGGC, ACGC, CCGC, CTGC, ACAA, ATAA, AAGA, ACGA, ATGA, AAAC, AGAC, ATCC, ACTC, ATTC, ACAT, GAAA, GGAA, GTCA, GTTA, GAAC, ATAT, TCGA
  • the four base pair DNA sequence is selected from the group consisting of GTGT, GTAT, TTAG, GTAG, TTAC, TCTC, TCAC, GTCC, GTAC, TCGC, AAGC, GAGC, GCGC, GTGC, TAGC, TTGC, ATGC, ACAC, ATAC, CTAA, CTAC, GTAA, GAGA, GTGA, GGAC, GTAC, GCGA, GCTT, GCTC, GC, GCAC, GCTA, GCAA and GCAT.
  • the DNA cleavage is in vitro. In other embodiments, the DNA cleavage is in vivo.
  • the DNA is selected from the group consisting of a PCR product; an artificial chromosome; genomic DNA isolated from bacteria, fungi, plants, or animal cells; and viral DNA.
  • the DNA is present in a cell selected from the group consisting of a bacterial, fungal, plant and animal cell.
  • the DNA is present in a nucleic acid selected from the group consisting of a plasmid, a prophage and a chromosome.
  • the method further comprises rationally-designing the I CreI derived meganuclease to recognize the recognition site.
  • the method further comprises producing the rationally-designed I-CreI-derived meganuclease.
  • the invention provides a cell transformed with a nucleic acid comprising, in order: a) a first 9 base pair DNA sequence which can be bound by an I CreI derived meganuclease monomer or by a first domain from a single-chain I CreI derived meganuclease; b) a four base pair DNA sequence selected from the group consisting of GTGT, GTAT, TTAG, GTAG, TTAC, TCTC, TCAC, GTCC, GTAC, TCGC, AAGC, GAGC, GCGC, GTGC, TAGC, TTGC, ATGC, ACAC, ATAC, CTAA, CTAC, GTAA, GAGA, GTGA, GGAC, GTAC, GCGA, GCTT, GCTC, GCGC, GCAC, GCTA, GCAA and GCAT; and c) a second 9 base pair DNA sequence which can be bound by an I CreI derived meganuclease monomer or by a second domain from
  • the invention provides a cell containing an exogenous nucleic acid sequence integrated into its genome, comprising, in order: a) a first exogenous 9 base pair DNA sequence which can be bound by an I CreI derived meganuclease monomer or by a first domain from a single-chain I CreI derived meganuclease; b) an exogenous four base pair DNA sequence selected from the group consisting of GTGT, GTAT, TTAG, GTAG, TTAC, TCTC, TCAC, GTCC, GTAC, TCGC, AAGC, GAGC, GCGC, GTGC, TAGC, TTGC, ATGC, ACAC, ATAC, CTAA, CTAC, GTAA, GAGA, GTGA, GGAC, GTAC, GCGA, GCTT, GCTC, GCGC, GCAC, GCTA, GCAA and GCAT; and a) a second exogenous 9 base pair DNA sequence which can be bound by an I CreI
  • the nucleic acid is a plasmid, an artificial chromosome, or a viral nucleic acid.
  • the cell is a non-human animal cell, a plant cell, a bacterial cell, or a fungal cell.
  • the four base pair DNA sequence is TTGT, TTAT, TCTT, TCGT, TCAT, GTTT, GTCT, GGAT, GAGT, GAAT, ATGT, TTTC, TTCC, TGAC, TAAC, GTTC, ATAT, TCGA, TTAA, GGGC, ACGC, CCGC, CTGC, ACAA, ATAA, AAGA, ACGA, ATGA, AAAC, AGAC, ATCC, ACTC, ATTC, ACAT, GAAA, GGAA, GTCA, GTTA, GAAC, ATAT, TCGA, TTAA, GCCC, GCGT, GCGG or GCAG.
  • the four base pair DNA sequence is GTGT, GTAT, TTAG, GTAG, TTAC, TCTC, TCAC, GTCC, GTAC, TCGC, AAGC, GAGC, GCGC, GTGC, TAGC, TTGC, ATGC, ACAC, ATAC, CTAA, CTAC, GTAA, GAGA, GTGA, GGAC, GTAC, GCGA, GCTT, GCTC, GCGC, GCAC, GCTA, GCAA or GCAT.
  • the invention provides a method of conducting a custom-designed, I-CreI-derived meganuclease business comprising: (a) receiving a DNA sequence into which a double-strand break is to be introduced by a rationally-designed I CreI-derived meganuclease; (b) identifying in the DNA sequence at least one recognition site for a rationally-designed I CreI-derived meganuclease with altered specificity relative to I-CreI, wherein the recognition site is not cleaved by a naturally-occurring I-CreI, wherein the recognition site has a four base pair central sequence selected from the group consisting of TTGT, TTAT, TCTT, TCGT, TCAT, GTTT, GTCT, GGAT, GAGT, GAAT, ATGT, TTTC, TTCC, TGAC, TAAC, GTTC, ATAT, TCGA, TTAA, GGGC, ACGC, CCGC, CTGC, ACAA, ATA
  • the method further comprises rationally-designing the I CreI derived meganuclease to recognize the recognition site.
  • the method further comprises producing the rationally-designed meganuclease.
  • the rationally-designed meganuclease is provided to the same party from which the DNA sequence has been received.
  • FIG. 1 Schematic illustration of the interactions between the naturally-occurring I-CreI homodimer and a double-stranded recognition sequence, based upon crystallographic data.
  • This schematic representation depicts one recognition sequence (SEQ ID NO: 2 and SEQ ID NO: 3), shown as unwound for illustration purposes only, bound by the homodimer, shown as two ovals.
  • the bases of each DNA half-site are numbered ⁇ 1 through ⁇ 9, and the amino acid residues of I-CreI which form the recognition surface are indicated by one-letter amino acid designations and numbers indicating residue position.
  • the four base pairs that comprise the center sequence are numbered +1 to +4.
  • Solid black lines hydrogen bonds to DNA bases.
  • SEQ ID NO: 2 and SEQ ID NO: 3 One wild-type I-CreI recognition sequence showing the locations of the inverted half-sites and center sequence.
  • FIG. 2 (A) Schematic diagram of the plasmid substrates evaluated to determine center sequence preference. A set of pUC-19 plasmids were produced which harbored potential recognition sequences for the genetically-engineered meganuclease DJ1. These potential recognition sequences comprised a pair of inverted DJ1 half-sites separated by a variety of different four base pair center sequences (numbered +1 through +4), as described below.
  • FIG. 3 (A) Schematic diagram of a T-DNA that was stably integrated into the Arabidopsis thaliana genome as described in Example 1.
  • a codon-optimized gene encoding the genetically-engineered BRP2 meganuclease (BRP2) (SEQ ID NO: 8) is under the control of a Hsp70 promoter (HSP) and a NOS terminator (TERM).
  • Hsp70 promoter Hsp70 promoter
  • TTERM NOS terminator
  • a pair of potential BRP2 recognition sequences (Site1, Site2) are housed adjacent to the terminator separated by 7 base pairs containing a PstI restriction enzyme site (PstI).
  • a kanamycin resistance marker (Kan) is also housed on the T-DNA to allow selection for stable transformants.
  • (B) The expected product following BRP2 meganuclease cleavage of Site1 and Site2 showing loss of the intervening 7 base pair fragment and PstI restriction site. Arrows show the location of PCR primers used to screen for cleavage of the T-DNA.
  • (C) Sequences of the BRP2 recognition sequences housed on either the GTAC construct (GTAC) or the TAGA construct (TAGA) with center sequences underlined.
  • (D) Example of electrophoresis data from a plant transformed with the GTAC construct. Genomic DNA was isolated from the leaves of Arabidopsis seedlings stably transformed with either the GTAC T-DNA construct before and after a 2 hour “heat-shock” to induce BRP2 expression.
  • FIG. 4 (A) Schematic diagram of a T-DNA that was stably integrated into the Arabidopsis thaliana genome as described in Example 2.
  • a codon-optimized gene encoding the BRP12-SC meganuclease (BRP12-SC) (SEQ ID NO: 15) is under the control of a Hsp70 promoter (HSP) and a NOS terminator (TERM).
  • Hsp70 promoter Hsp70 promoter
  • TTERM NOS terminator
  • a pair of potential BRP12-SC recognition sequences (Site1, Site2) are housed adjacent to the terminator separated by 7 base pairs containing a PstI restriction enzyme site (PstI).
  • a kanamycin resistance marker (Kan) is also housed on the T-DNA to allow selection for stable transformants.
  • (B) The expected product following BRP12-SC meganuclease cleavage of Site1 and Site2 showing loss of the intervening 7 base pair fragment and PstI restriction site. Arrows show the location of PCR primers used to screen for cleavage of the T-DNA.
  • C Sequences of the BRP12-SC recognition sequences housed on either the GTAC construct (GTAC) or the TAGA construct (TAGA) with center sequences underlined.
  • FIG. 5 Graphic representation of the effects of meganuclease concentration and center sequence on in vitro meganuclease cleavage.
  • the BRP2 meganuclease (SEQ ID NO: 8, see Example 1) was added at the indicated concentration to a digest reaction containing 0.25 picomoles of a plasmid substrate harboring either a BRP2 recognition sequence with the center sequence GTAC or a BRP2 recognition sequence with the center sequence TAGA.
  • Reactions were 25 microliters in SA buffer (25 mM Tris-HCL, pH 8.0, 100 mM NaCl, 5 mM MgCl 2 , 5 mM EDTA). Reactions were incubated at 37° C. for 2 hours and were then visualized by gel electrophoresis and the percent of plasmid substrate cleaved by the meganuclease was plotted as a function of meganuclease concentration.
  • SA buffer 25 mM Tris-HCL,
  • the present invention is based, in part, upon the identification and characterization of particular DNA sequences that are more efficiently cleaved by the rationally-designed, I-CreI-derived meganucleases.
  • the invention is based on the discovery that certain four-base pair DNA sequences, when incorporated as the central four-base pairs of a rationally-designed, I-CreI-derived meganuclease recognition sequence, can significantly impact cleavage by the corresponding meganuclease although the meganuclease does not, based upon analysis of crystal structures, appear to contact the central four base pairs.
  • there are four DNA bases (A, C, G, and T) there are 4 4 or 256 possible DNA sequences that are four base pairs in length.
  • I-CreI-derived meganuclease refers to a rationally-designed (i.e., genetically-engineered) meganuclease that is derived from I-CreI.
  • genetically-engineered meganuclease refers to a recombinant variant of an I-CreI homing endonuclease that has been modified by one or more amino acid insertions, deletions or substitutions that affect one or more of DNA-binding specificity, DNA cleavage activity, DNA-binding affinity, and/or dimerization properties.
  • Some genetically-engineered meganucleases are known in the art (see, e.g., Porteus et al. (2005), Nat. Biotechnol. 23: 967-73; Sussman et al. (2004), J. Mol. Biol. 342: 31-41; Epinat et al. (2003), Nucleic Acids Res. 31: 2952-62) and a general method for rationally-designing such variants is disclosed in WO 2007/047859.
  • a meganuclease may bind to double-stranded DNA as a homodimer, as is the case for wild-type I-CreI, or it may bind to DNA as a heterodimer.
  • a meganuclease may also be a “single-chain heterodimer” in which a pair of DNA-binding domains derived from I-CreI are joined into a single polypeptide using a peptide linker.
  • the term “homing endonuclease” is synonymous with the term “meganuclease.”
  • rationally-designed means non-naturally occurring and/or genetically engineered.
  • the rationally-designed meganucleases of the invention differ from wild-type or naturally-occurring meganucleases in their amino acid sequence or primary structure, and may also differ in their secondary, tertiary or quaternary structure.
  • the rationally-designed meganucleases of the invention also differ from wild-type or naturally-occurring meganucleases in recognition sequence-specificity and/or activity.
  • the term “recombinant” means having an altered amino acid sequence as a result of the application of genetic engineering techniques to nucleic acids which encode the protein, and cells or organisms which express the protein.
  • nucleic acid means having an altered nucleic acid sequence as a result of the application of genetic engineering techniques.
  • Genetic engineering techniques include, but are not limited to, PCR and DNA cloning technologies; transfection, transformation and other gene transfer technologies; homologous recombination; site-directed mutagenesis; and gene fusion.
  • a protein having an amino acid sequence identical to a naturally-occurring protein, but produced by cloning and expression in a heterologous host is not considered recombinant.
  • the term “genetically-modified” refers to a cell or organism in which, or in an ancestor of which, a genomic DNA sequence has been deliberately modified by recombinant technology. As used herein, the term “genetically-modified” encompasses the term “transgenic.”
  • wild-type refers to any naturally-occurring form of a meganuclease.
  • wild-type is not intended to mean the most common allelic variant of the enzyme in nature but, rather, any allelic variant found in nature. Wild-type meganucleases are distinguished from recombinant or non-naturally-occurring meganucleases.
  • the term “recognition sequence half-site” or simply “half site” means a 9 base pair DNA sequence which is recognized by a meganuclease monomer, in the case of a dimeric meganuclease, or by one domain of a single-chain meganuclease.
  • recognition sequence refers to a pair of half-sites which is bound and cleaved by a meganuclease.
  • a recognition sequence comprises a pair of inverted, 9 base pair half sites separated by four base-pairs.
  • the recognition sequence is, therefore, 22 base-pairs in length.
  • the base pairs of each half-site are designated ⁇ 9 through ⁇ 1, with the ⁇ 9 position being most distal from the cleavage site and the ⁇ 1 position being adjacent to the 4 base pair center sequence, the base pairs of which are designated +1 through +4.
  • each half-site which is oriented 5′ to 3′ in the direction from ⁇ 9 to ⁇ 1 (i.e., towards the cleavage site), is designated the “sense” strand, and the opposite strand is designated the “antisense strand”, although neither strand may encode protein.
  • the “sense” strand of one half-site is the antisense (opposite) strand of the other half-site. See, for example, FIG. 1 a.
  • center sequence refers to the four base pairs separating half sites in the meganuclease recognition sequence. These bases are numbered +1 through +4 in FIG. 1 a.
  • the center sequence comprises the four bases that become the 3′ single-strand overhangs following meganuclease cleavage.
  • Center sequence can refer to the sequence of the sense strand or the antisense (opposite) strand.
  • the term “specificity” refers to the ability of a meganuclease to recognize and cleave double-stranded DNA molecules only at a particular subset of all possible recognition sequences.
  • the set of recognition sequences will share certain conserved positions or sequence motifs, but may be degenerate at one or more positions.
  • a more specific meganuclease is capable of binding and cleaving a smaller subset of the possible recognition sequences, whereas a less specific meganuclease is capable of binding and cleaving a larger subset of the possible recognition sequences.
  • palindromic refers to a recognition sequence consisting of inverted repeats of identical half-sites. In this case, however, the palindromic sequence need not be palindromic with respect to the center sequence, which is not contacted by the enzyme. In the case of dimeric meganucleases, palindromic DNA sequences are recognized by homodimers in which the two monomers make contacts with identical half-sites.
  • the term “pseudo-palindromic” refers to a recognition sequence consisting of inverted repeats of non-identical or imperfectly palindromic half-sites.
  • the pseudo-palindromic sequence need not be palindromic with respect to the center sequence, and also can deviate from a perfectly palindromic sequence between the two half-sites.
  • Pseudo-palindromic DNA sequences are typical of the natural DNA sites recognized by wild-type homodimeric meganucleases in which two identical enzyme monomers make contacts with different half-sites.
  • non-palindromic refers to a recognition sequence composed of two unrelated half-sites of a meganuclease.
  • the non-palindromic sequence need not be palindromic with respect to either the center sequence or the two monomer half-sites.
  • Non-palindromic DNA sequences are recognized by either heterodimeric meganucleases or single-chain meganucleases comprising a pair of domains that recognize non-identical half-sites.
  • the term “activity” refers to the rate at which a meganuclease of the invention cleaves a particular recognition sequence. Such activity is a measurable enzymatic reaction, involving the hydrolysis of phosphodiester bonds of double-stranded DNA.
  • the activity of a meganuclease acting on a particular DNA substrate is affected by the affinity or avidity of the meganuclease for that particular DNA substrate which is, in turn, affected by both sequence-specific and non-sequence-specific interactions with the DNA.
  • homologous recombination refers to the natural, cellular process in which a double-stranded DNA-break is repaired using a homologous DNA sequence as the repair template (see, e.g., Cahill et al. (2006), Front. Biosci. 11:1958-1976).
  • the homologous DNA sequence may be an endogenous chromosomal sequence or an exogenous nucleic acid that was delivered to the cell.
  • a meganuclease is used to cleave a recognition sequence within a target sequence in a genome and an exogenous nucleic acid with homology to or substantial sequence similarity with the target sequence is delivered into the cell and used as a template for repair by homologous recombination.
  • the DNA sequence of the exogenous nucleic acid which may differ significantly from the target sequence, is thereby incorporated into the chromosomal sequence.
  • the process of homologous recombination occurs primarily in eukaryotic organisms.
  • the term “homology” is used herein as equivalent to “sequence similarity” and is not intended to require identity by descent or phylogenetic relatedness.
  • non-homologous end-joining refers to the natural, cellular process in which a double-stranded DNA-break is repaired by the direct joining of two non-homologous DNA segments (see, e.g., Cahill et al. (2006), Front. Biosci. 11:1958-1976). DNA repair by non-homologous end joining is error-prone and frequently results in the untemplated addition or deletion of DNA sequences at the site of repair.
  • a meganuclease can be used to produce a double-stranded break at a meganuclease recognition sequence within a target sequence in a genome to disrupt a gene (e.g., by introducing base insertions, base deletions, or frameshift mutations) by non-homologous end joining
  • an exogenous nucleic acid lacking homology to or substantial sequence similarity with the target sequence may be captured at the site of a meganuclease-stimulated double-stranded DNA break by non-homologous end joining (see, e.g., Salomon et al. (1998), EMBO J. 17:6086-6095).
  • the process of non-homologous end joining occurs in both eukaryotes and prokaryotes such as bacteria.
  • sequence of interest means any nucleic acid sequence, whether it codes for a protein, RNA, or regulatory element (e.g., an enhancer, silencer, or promoter sequence), that can be inserted into a genome or used to replace a genomic DNA sequence using a meganuclease protein.
  • Sequences of interest can have heterologous DNA sequences that allow for tagging a protein or RNA that is expressed from the sequence of interest.
  • a protein can be tagged with tags including, but not limited to, an epitope (e.g., c-myc, FLAG) or other ligand (e.g., poly-His).
  • a sequence of interest can encode a fusion protein, according to techniques known in the art (see, e.g., Ausubel et al., Current Protocols in Molecular Biology, Wiley 1999).
  • the sequence of interest is flanked by a DNA sequence that is recognized by the meganuclease for cleavage.
  • the flanking sequences are cleaved allowing for proper insertion of the sequence of interest into genomic recognition sequences cleaved by a meganuclease.
  • the entire sequence of interest is homologous to or has substantial sequence similarity with a target sequence in the genome such that homologous recombination effectively replaces the target sequence with the sequence of interest.
  • the sequence of interest is flanked by DNA sequences with homology to or substantial sequence similarity with the target sequence such that homologous recombination inserts the sequence of interest within the genome at the locus of the target sequence.
  • the sequence of interest is substantially identical to the target sequence except for mutations or other modifications in the meganuclease recognition sequence such that the meganuclease can not cleave the target sequence after it has been modified by the sequence of interest.
  • single-chain meganuclease refers to a polypeptide comprising a pair of meganuclease subunits joined by a linker.
  • a single-chain meganuclease has the organization: N-terminal subunit—Linker—C-terminal subunit.
  • the two meganuclease subunits, each of which is derived from I-CreI, will generally be non-identical in amino acid sequence and will recognize non-identical half-sites.
  • single-chain meganucleases typically cleave pseudo-palindromic or non-palindromic recognition sequences.
  • a single chain meganuclease may be referred to as a “single-chain heterodimer” or “single-chain heterodimeric meganuclease” although it is not, in fact, dimeric.
  • the present invention is based, in part, in the identification of subsets of the possible four base pair center sequences that are preferred by I-CreI-derived meganucleases.
  • the wild-type enzyme does not make significant contacts with the bases in the center sequence, the same center sequence preferences of the wild-type I-CreI homing nuclease apply to rationally-designed I-CreI-derived meganucleases which have been redesigned with respect to, for example, half-site preference, DNA-binding affinity, and/or heterodimerization ability.
  • This invention provides, therefore, important criteria that can be considered in determining whether or not a particular 22 base pair DNA sequence is a suitable I-CreI-derived meganuclease recognition sequence.
  • DJ1 is a homodimeric I-CreI-derived meganuclease which was designed to recognize a palindromic meganuclease recognition sequence (SEQ ID NO: 5, SEQ ID NO: 6) that differs at 4 positions per half-site relative to wild-type I-CreI. This change in half-site specificity was achieved by the introduction of 6 amino acid substitutions to wild type I-CreI (K28D, N30R, S32N, Q38E, S40R, and T42R).
  • DJ1 was expressed in E. coli and purified as described in Example 1 of WO 2007/047859. Then, 25 picomoles of purified meganuclease protein were added to a 10 nM solution of plasmid DNA substrate in SA buffer (25 mM Tris-HCL, pH 8.0, 100 mM NaCl, 5 mM MgCl 2 , 5 mM EDTA) in a 25 microliter reaction. 1 microliter of XmnI restriction enzyme was added to linearize the plasmid substrates. Reactions were incubated at 37° C. for 4 hours and were then visualized by gel electrophoresis to determine the extent to which each was cleaved by the DJ1 meganuclease.
  • SA buffer 25 mM Tris-HCL, pH 8.0, 100 mM NaCl, 5 mM MgCl 2 , 5 mM EDTA
  • the plasmid substrates used in these experiments comprised a pUC-19 plasmid in which a potential meganuclease recognition sequence was inserted into the polylinker site (SmaI site).
  • Each potential meganuclease recognition site comprised a pair of inverted DJ1 half-sites (SEQ ID NO: 7) separated by a different center sequence.
  • center sequence preference There are 4 4 or 256 possible center sequences. Of these, 25%, or 64, have a purine base at N +2 and pyrimidine at N +3 and, therefore, were eliminated as center sequences based on the experiment described above. Of the remaining 192, 92 are redundant because meganucleases are symmetric and recognize bases equally on both the sense and antisense strand.
  • the sequence A +1 A +2 A +3 A +4 on the sense strand is recognized by the meganuclease as T +1 T ⁇ 2 T +3 T +4 on the antisense strand and, thus, A +1 A +2 A +3 A +4 and T +1 T +2 T +3 T +4 are functionally equivalent.
  • N +2 /N +3 conflicts there were 100 possible center sequences remaining. To determine which of these were preferred by meganucleases, we produced 100 plasmid substrates harboring these 100 center sequences flanked by inverted recognition half-sites for the DJ1 meganuclease. DJ1 was then incubated with each of the 100 plasmids and cleavage activity was evaluated as described above.
  • each of the center sequences listed in Table 2 is equivalent to its opposite strand sequence due to the fact that the I-CreI meganuclease binds its recognition sequence as a symmetric homodimer.
  • sequence no. 100 in Table 2 C +1 T +2 G +3 C +4 , is equivalent to its opposite strand sequence, G +1 C +2 A +3 G +4 .
  • preferred center sequences have the form G + N +2 R +3 X +4 where Y is a pyrimidine (C or T), R is a purine (A or G), and X is any base (A, C, G, or T).
  • in vitro DNA cleavage conditions are, in general, less stringent than conditions in vivo, the use of sub-optimal center sequences may be acceptable for such applications.
  • in vitro digests using engineered meganucleases can be performed at a higher ratio of meganuclease to DNA, there is typically less non-specific (genomic) DNA competing for meganuclease, and solution conditions can be optimized to favor meganuclease cleavage (e.g., using SA buffer as described above).
  • SA buffer as described above
  • a preferred I-CreI-derived meganuclease recognition sequence for in vitro applications will comprise: (1) a first 9 base pair half-site amenable to recognition by a meganuclease monomer (or a first domain of a single-chain meganuclease); (2) a preferred or most preferred center sequence from Table 2 or Table 3; and (3) a second 9 base pair half-site amenable to recognition by a meganuclease monomer (or a second domain of a single-chain meganuclease) in the reverse orientation relative to the first half-site.
  • the invention provides methods for cleaving a double-stranded DNA in vitro by (a) identifying at least one potential recognition site for at least one I-CreI-derived meganuclease within the DNA, wherein the potential recognition site has a four base pair central sequence selected from the group of central sequences of Table 2; (b) identifying an I-CreI-derived meganuclease which recognizes that recognition site in the DNA; and (c) contacting the I-CreI-derived meganuclease with the DNA; whereby the I-CreI meganuclease cleaves the DNA.
  • the invention provides methods for cleaving a double-stranded DNA in vitro by (a) introducing into the DNA a recognition site for an I-CreI-derived meganuclease having a four base pair central sequence selected from the group consisting of central sequences of Table 2; and (b) contacting the I-CreI-derived meganuclease with the DNA; whereby the I-CreI-derived meganuclease cleaves the DNA.
  • the DNA is selected from a PCR product; an artificial chromosome; genomic DNA isolated from bacteria, fungi, plants, or animal cells; and viral DNA.
  • the DNA is present in a nucleic acid selected from a plasmid, a prophage and a chromosome.
  • the four base pair DNA sequence is selected from Table 3. In other embodiments, the four base pair DNA sequence is selected from Table 4.
  • the I-CreI-derived meganuclease can be specifically designed for use with the chosen recognition site in the method.
  • a preferred in vivo meganuclease recognition sequence will comprise: (1) a first 9 base pair half-site amenable to recognition by a meganuclease monomer (or a first domain of a single-chain meganuclease); (2) a preferred center sequence from Table 5; and (3) a second 9 base pair half-site amenable to recognition by a meganuclease monomer (or a second domain of a single-chain meganuclease) in the reverse orientation relative to the first half-site.
  • the invention provides methods for cleaving a double-stranded DNA in vivo by (a) identifying at least one potential recognition site for at least one I-CreI-derived meganuclease within the DNA, wherein the potential recognition site has a four base pair central sequence selected from the group of central sequences of Table 2; (b) identifying an I-CreI-derived meganuclease which recognizes that recognition site in the DNA; and (c) contacting the I-CreI-derived meganuclease with the DNA; whereby the I-CreI-derived meganuclease cleaves the DNA.
  • the invention provides methods for cleaving a double-stranded DNA in vivo by (a) introducing into the DNA a recognition site for an I-CreI-derived meganuclease having a four base pair central sequence selected from the group consisting of central sequences of Table 2; and (b) contacting the I-CreI-derived meganuclease with the DNA; whereby the I-CreI-derived meganuclease cleaves the DNA.
  • the DNA is present in a cell selected from a bacterial, fungal, plant and animal cell.
  • the DNA is present in a nucleic acid selected from a plasmid, a prophage and a chromosome.
  • the four base pair DNA sequence is selected from Table 3. In other embodiments, the four base pair DNA sequence is selected from Table 4.
  • the I-CreI-derived meganuclease is specifically designed for use with the chosen recognition site in the methods of the invention.
  • the method includes the additional step of rationally-designing the I-CreI-derived meganuclease to recognize the chosen recognition site. In some embodiments, the method further comprises producing the I-CreI-derived meganuclease.
  • the invention provides cells transformed with a nucleic acid including (a) a first 9 base pair DNA sequence which can be bound by an I-CreI-derived meganuclease monomer or by a first domain from a single-chain I-CreI-derived meganuclease; (b) a four base pair DNA sequence selected from Table 2; and (c) a second 9 base pair DNA sequence which can be bound by an I-CreI-derived meganuclease monomer or by a second domain from a single-chain I-CreI-derived meganuclease; wherein the second 9 base pair DNA sequence is in the reverse orientation relative to the first.
  • the invention provides a cell containing an exogenous nucleic acid sequence integrated into its genome, including, in order: (a) a first exogenous 9 base pair DNA sequence which can be bound by an I-CreI-derived meganuclease monomer or by a first domain from a single-chain I-CreI-derived meganuclease; (b) an exogenous four base pair DNA sequence selected from Table 2; and (c) a second exogenous 9 base pair DNA sequence which can be bound by an I-CreI-derived meganuclease monomer or by a second domain from a single-chain I-CreI-derived meganuclease; wherein the second 9 base pair DNA sequence is in the reverse orientation relative to the first.
  • the invention provides a cell containing an exogenous nucleic acid sequence integrated into its genome, including, in order: (a) a first exogenous 9 base pair DNA sequence which can be bound by an I-CreI-derived meganuclease monomer or by a first domain from a single-chain I-CreI-derived meganuclease; (b) an exogenous two base pair DNA sequence, wherein the two base pairs correspond to bases N +1 and N +2 of a four base pair DNA sequence selected from Table 2; (c) an exogenous DNA sequence comprising a coding sequence which is expressed in the cell; (d) an exogenous two base pair DNA sequence, wherein the two base pairs correspond to bases N +3 and N +4 of a four base pair DNA sequence selected from Table 2; and (e) a second exogenous 9 base pair DNA sequence which can be bound by the I-CreI-derived meganuclease monomer or by a second domain from the single-chain I-CreI-
  • the nucleic acid is a plasmid. In other embodiments, the nucleic acid is an artificial chromosome. In other embodiments, the nucleic acid is integrated into the genomic DNA of the cell. In other embodiments, the nucleic acid is a viral nucleic acid.
  • the cell is selected from the group a human cell, a non-human animal cell, a plant cell, a bacterial cell, and a fungal cell.
  • the four base pair DNA sequence is selected from Table 3. In other embodiments, the four base pair DNA sequence is selected from Table 4.
  • the I-CreI meganuclease is specifically designed for use with the chosen recognition site in the methods of the invention.
  • a meganuclease business can be conducted based on I-CreI-derived meganucleases.
  • such business can operate as following.
  • the business received a DNA sequence into which a double-strand break is to be introduced by a rationally-designed I CreI-derived meganuclease.
  • the business identifies in the DNA sequence at least one recognition site for a rationally-designed I CreI-derived meganuclease with altered specificity relative to I-CreI, wherein the recognition site is not cleaved by a naturally-occurring I-CreI, wherein the recognition site has a four base pair central sequence selected from the group consisting of TTGT, TTAT, TCTT, TCGT, TCAT, GTTT, GTCT, GGAT, GAGT, GAAT, ATGT, TTTC, TTCC, TGAC, TAAC, GTTC, ATAT, TCGA, TTAA, GGGC, ACGC, CCGC, CTGC, ACAA, ATAA, AAGA, ACGA, ATGA, AAAC, AGAC, ATCC, ACTC, ATTC, ACAT, GAAA, GGAA, GTCA, GTTA, GAAC, ATAT, TCGA, TTAA, GCCC, GCGG and GCAG.
  • the business rationally-designs an I-CreI-derived meganuclease that cleaves the recognition site in the DNA.
  • the business produces the rationally-designed I-CreI-derived meganuclease.
  • the center sequences GTAC, ACAC, and GTGA have previously been shown to be effective center sequences for in vitro and in vivo applications. These center sequences are specifically excluded from some aspects of the present invention.
  • the center sequences TTGA and GAAA have previously been shown to be poor center sequences for in vivo applications (Arnould, et al. (2007). J. Mol. Biol. 371: 49-65).
  • Examples 1 and 2 refer to engineered meganucleases cleaving optimized meganuclease recognition sites in vivo in a model plant system.
  • Example 3 refers to an engineered meganuclease cleaving optimized meganuclease recognition sites in vitro.
  • BRP2 An engineered meganuclease called BRP2 (SEQ ID NO: 8) was produced using the method disclosed in WO 2007/047859.
  • This meganuclease is derived from I-CreI and was engineered to recognize DNA sites that are not recognized by wild-type I-CreI (e.g., BRP2 recognition sequences include SEQ ID NO: 9 and SEQ ID NO: 10, or SEQ ID NO: 11 and SEQ ID NO: 12).
  • an SV40 nuclear localization signal was added to the N-terminus of the protein.
  • T-DNA constructs Two such T-DNA constructs were produced which varied the center sequence of the meganuclease recognition sequences flanking the PstI restriction enzyme site ( FIG. 3 c ).
  • the meganuclease recognition sites had the center sequence GTAC (a preferred in vivo center sequence, Table 5, sequence 9; SEQ ID NO: 9 and SEQ ID NO 10).
  • the second construct (the “TAGA construct”) had the center sequence TAGA (a non-preferred center sequence, opposite strand sequence to Table 2, sequence 77; SEQ ID NO: 11 and SEQ ID NO 12).
  • Stably transformed Arabidopsis plants carrying each construct were produced by selection for a kanamycin resistance marker housed on the T-DNA. Genomic DNA was then isolated from the transformed plants (by leaf punch) before and after heat-shock to induce BRP2 meganuclease expression. Genomic DNA samples were added to PCR reactions using primers to amplify the region of the T-DNA housing the meganuclease recognition sequences. PCR products were then digested with PstI and visualized by gel electrophoresis ( FIG. 3 d ). Results are summarized in Table 6.
  • PCR sample in which a significant percentage (>25%) of product was found to be resistant to PstI was considered to be indicative of in vivo meganuclease cleavage in that particular plant and was scored as “cut” in Table 6. It was found that, prior to heat-shock, the vast majority of PCR samples from plants carrying either construct retained the PstI site. After heat-shock, however, a large percentage of samples taken from plants transformed with the GTAC construct, but not the TAGA construct, had lost the PstI site. PCR products from the GTAC construct-transformed plants lacking a PstI site were cloned into a pUC-19 plasmid and sequenced.
  • the engineered meganuclease BRP12-SC (SEQ ID NO: 15) was produced in accordance with WO 2007/047859, except that this meganuclease is a single-chain heterodimer.
  • wild-type I-CreI binds to and cleaves DNA as a homodimer.
  • the natural recognition sequence for I-CreI is pseudo-palindromic.
  • the BRP12-SC recognition sequences are non-palindromic (e.g., SEQ ID NO: 16 and SEQ ID NO: 17, or SEQ ID NO: 18 and SEQ ID NO: 19).
  • an engineered meganuclease heterodimer comprising a pair of subunits each of which recognizes one half-site within the full-length recognition sequence.
  • the two engineered meganuclease monomers are physically linked to one another using an amino acid linker to produce a single-chain heterodimer.
  • This linker comprises amino acids 166-204 (SEQ ID NO: 20) of BRP12-SC.
  • the linker sequence joins an N-terminal meganuclease subunit terminated at L165 (corresponding to L155 of wild-type I-CreI) with a C-terminal meganuclease subunit starting at K204 (corresponding to K7 of wild-type I-CreI).
  • the benefits of physically linking the two meganuclease monomers using this novel linker is twofold: First, it ensures that the meganuclease monomers can only associate with one another (heterodimerize) to cut the non-palindromic BRP12-SC recognition sequence rather than also forming homodimers which can recognize palindromic or pseudopalindromic DNA sites that differ from the BRP12-SC recognition sequence.
  • the physical linking of meganuclease monomers obviates the need to express two monomers simultaneously in the same cell to obtain the desired heterodimer. This significantly simplifies vector construction in that it only requires a single gene expression cassette.
  • the BRP12-SC meganuclease has an SV40 nuclear localization signal (SEQ ID NO: 13) at its N-terminus.
  • T-DNA constructs Two such T-DNA constructs were produced which varied only in the center sequences of the meganuclease recognition sequences flanking the PstI restriction enzyme site ( FIG. 4 c ).
  • the meganuclease recognition sites had the center sequence GTAC (a preferred in vivo center sequence, Table 5, sequence 9; SEQ ID NO: 16 and SEQ ID NO 17).
  • the second construct (the “TAGA construct”) had the center sequence TAGA (a non-preferred center sequence, opposite strand sequence to Table 2, sequence 77; SEQ ID NO: 18 and SEQ ID NO 19).
  • Stably transformed Arabidopsis plants carrying each construct were produced by selection for a kanamycin resistance marker housed on the T-DNA. Genomic DNA was then isolated from the transformed plants (by leaf punch) before and after heat-shock to induce BRP12-SC meganuclease expression. Genomic DNA samples were added to PCR reactions using primers to amplify the region of the T-DNA housing the meganuclease recognition sequences. PCR products were then digested with PstI and visualized by gel electrophoresis. The results of this analysis are presented in Table 7.
  • the BRP2 meganuclease described in Example 1 (SEQ ID NO: 8) was expressed in E. coli and purified as in Example 1 of WO 2007/047859. The purified meganuclease was then added at varying concentrations to reactions containing plasmids harboring BRP2 recognition sequences with either a GTAC or TAGA center sequence (0.25 picomoles of plasmid substrate in 25 microliters of SA buffer: 25 mM Tris-HCL, pH 8.0, 100 mM NaCl, 5 mM MgCl 2 , 5 mM EDTA). Reactions were incubated at 37° C.

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US20230088311A1 (en) 2023-03-23
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US20170298420A1 (en) 2017-10-19
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US20150050655A1 (en) 2015-02-19
US20190194729A1 (en) 2019-06-27
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DK3211075T3 (en) 2019-01-21
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