# Patent

## Title
Repeat variable diresidues for targeting nucleotides

## Abstract

The present invention relates to polypeptides and more particularly to Transcription Activator-Like Effector derived proteins that allow to efficiently target and/or process nucleic acids. The present invention also concerns methods to use these proteins. The present invention also relates to vectors, compositions and kits in which RVD domains and Transcription Activator-Like Effector (TALE) proteins of the present invention are used.

## Background
FIELD OF THE INVENTION
The present invention relates to polypeptides and more particularly to Transcription Activator-Like Effector derived proteins that allow to efficiently target and/or process nucleic acids. The present invention also concerns methods to use these proteins. The present invention also relates to vectors, compositions and kits in which Repeat Variable Diresidue (RVD) domains and Transcription Activator-Like Effector (TALE) proteins of the present invention are used.
BACKGROUND OF THE INVENTION
The DNA binding domain of a recently discovered new class of protein derived from Transcription Activator-Like Effectors (TALE), has been widely used for several applications in the field of genome engineering. The sequence specificity of this family of proteins used in the infection process by plant pathogens of the Xanthomonas genus is driven by an array of motifs of 33-35 amino acids repeats, differing essentially by the two positions 12 and 13 (Boch, Scholze et al. 2009; Moscou and Bogdanove 2009). The recent achievement of the high resolution structure of TAL effectors bound to DNA showed that each single base of the same strand in the DNA target is contacted by a single repeat (Deng, Yan et al. 2012; Mak, Bradley et al. 2012), with the specificity resulting from the two polymorphic amino acids of the repeat; the so-called RVDs (Repeat Variable Diresidue). The modularity of these DNA binding domains has been confirmed to a certain extent by assembly of designed TALE-derived protein with new specificities.
TAL effectors fused to a nuclease catalytic head (TALE-nuclease) to create new tools, especially for genome engineering applications have been shown to be active to various extents in cell-based assays in yeast, mammalian cells and plants (Christian, Cermak et al. 2010; Cermak, Doyle et al. 2011; Geissler, Scholze et al. 2011; Huang, Xiao et al. 2011; Li, Huang et al. 2011; Mahfouz, Li et al. 2011; Miller, Tan et al. 2011; Morbitzer, Elsaesser et al. 2011; Mussolino, Morbitzer et al. 2011; Sander, Cade et al. 2011; Tesson, Usal et al. 2011; Weber, Gruetzner et al. 2011; Zhang, Cong et al. 2011; Li, Piatek et al. 2012; Mahfouz, Li et al. 2012).
Despite the description in the literature of a dozen of natural RVDs and their predicted partner bases, researchers are mainly focusing on using four different RVD/base couples NI/A, HD/C, NN/G, and NG/T [(Huang, Xiao et al. 2011; Mahfouz, Li et al. 2011; Morbitzer, Elsaesser et al. 2011; Mussolino, Morbitzer et al. 2011; Mahfouz, Li et al. 2012; Mak, Bradley et al. 2012)]. In a previous study, the DNA binding specificity of alternative RVDs which target the base at the 6th position have been tested (WO 2011/146121).
Moreover, up to now, researchers have only published successful use of TALE-nucleases without reporting how frequently a TALE-nuclease fails to work. The designs of these arrays still only relay on the published code (Boch, Scholze et al. 2009; Moscou and Bogdanove 2009) and in fact lead to a certain amount of inactive or weakly active molecules. There remains a need for designing new RVDs obeying to an improved code, allowing governing TALE/DNA interactions with high specificity and/or flexibility.
Here, the inventors have made the conjecture that new RVDs could replace existing ones by testing their binding to nucleotide bases at the first to the fourth positions of a TALE recognition domain and that this replacement could improve the overall specificity TALE nucleic acid recognition. By proceeding accordingly, the inventors identified a set of new RVDs with useful activity and specificity.
BRIEF SUMMARY OF THE INVENTION
In a general aspect, the present invention relates to polypeptides that allow to efficiently target and/or process nucleic acids. More particularly the present invention relates to Transcription Activator-Like Effector derived proteins and particularly to repeat sequences comprising highly specific Repeat Variable-Diresidue (RVD) that allow to efficiently target and process nucleic acids. The present invention also concerns methods to use these RVDs and Transcription Activator-Like Effector proteins or chimeric proteins comprising these repeat sequences with RVDs. The present invention also relates to vectors, compositions and kits in which RVDs and Transcription Activator-Like Effector proteins of the present invention are used.



BRIEF DESCRIPTION OF THE FIGURES AND TABLES
In addition to the preceding features, the invention further comprises other features which will emerge from the description which follows, as well as to the appended drawings. A more complete appreciation of the invention and many of the attendant advantages thereof will be readily obtained as the same becomes better understood by reference to the following Figures in conjunction with the detailed description below.
FIG. 1: Schematic representation of the solid support method for synthesizing RVDs arrays used to prepare the libraries 1 to 8.
FIG. 2: Schematic representation of the solid support method for synthesizing RVDs arrays used to prepare the libraries A, B, C and D.
FIG. 3: a-c: TALE-Nuclease cleavage activity levels of individual clones of the library A on their respective targets (SEQ ID NO: 94 to SEQ ID NO: 97) containing A, C, G or T at the position 1 of the TALE array in our yeast SSA assay previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006). Values are comprised between 0 and 1. Maximal value is 1.
FIG. 4: a-c: TALE-Nuclease cleavage activity levels of individual clones of the library B on their respective targets (SEQ ID NO: 98 to SEQ ID NO: 101) containing A, C, G or T at the position 2 of the TALE array in our yeast SSA assay previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006). Values are comprised between 0 and 1. Maximal value is 1.
FIG. 5: a-d: TALE-Nuclease cleavage activity levels of individual clones of the library C on their respective targets (SEQ ID NO: 102 to SEQ ID NO: 105) containing A, C, G or T at the position 3 of the TALE array our yeast SSA assay previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006). Values are comprised between 0 and 1. Maximal value is 1.
FIG. 6: a-c: TALE-Nuclease cleavage activity levels of individual clones of the library D on their respective targets (SEQ ID NO: 106 to SEQ ID NO: 109) containing A, C, G or T at the position 4 of the TALE array our yeast SSA assay previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006). Values are comprised between 0 and 1. Maximal value is 1.



Table 1: List of oligonucleotides (5′→3′) used to introduce diversity in positions 12 and 13 in libraries of a HD bloc in example 1.
Table 2: Target collections for libraries screening in example 1.
Table 3: Mean activities of three clones with one RVD randomized on a series of targets (SEQ ID NO: 62-77) in our yeast SSA assay previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) at 30° C. − indicates no detectable activity, + indicates low activity, ++ medium activity and +++ high activity.
Table 4: List of oligonucleotides (5′→3′) used to introduce diversity in position 12 and 13 of a NG bloc in example 2.
Table 5: List of pseudo-palindromic sequences targets (two identical recognition sequences are placed facing each other on both DNA strands) in our yeast SSA assay previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) at 30° C., used for activity screens in yeast of libraries A, B, C and D.
Table 6: List of heterodimeric sequences targets (two different recognition sequences are placed facing each other on both DNA strands) in our yeast SSA assay previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) at 37° C., used for activity screens in yeast of NM/LP and SD/VG containing half-TALE-Nuclease.
Table 7: Activities of the three TALE-Nuclease pairs on heterodimeric sequence target A and B (two identical recognition sequences are placed facing each other on both DNA strands) in our yeast SSA assay previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) at 30° C. ++ indicates medium activity and +++ high activity.
DETAILED DESCRIPTION OF THE INVENTION
Unless specifically defined herein, all technical and scientific terms used have the same meaning as commonly understood by a skilled artisan in the fields of gene therapy, biochemistry, genetics, and molecular biology.
All methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, with suitable methods and materials being described herein. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will prevail. Further, the materials, methods, and examples are illustrative only and are not intended to be limiting, unless otherwise specified.
The practice of the present invention will employ, unless otherwise indicated, conventional techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. See, for example, Current Protocols in Molecular Biology (Frederick M. AUSUBEL, 2000, Wiley and son Inc, Library of Congress, USA); Molecular Cloning: A Laboratory Manual, Third Edition, (Sambrook et al, 2001, Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press); Oligonucleotide Synthesis (M. J. Gait ed., 1984); Mullis et al. U.S. Pat. No. 4,683,195; Nucleic Acid Hybridization (B. D. Harries & S. J. Higgins eds. 1984); Transcription And Translation (B. D. Hames & S. J. Higgins eds. 1984); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide To Molecular Cloning (1984); the series, Methods In ENZYMOLOGY (J. Abelson and M. Simon, eds.-in-chief, Academic Press, Inc., New York), specifically, Vols. 154 and 155 (Wu et al. eds.) and Vol. 185, “Gene Expression Technology” (D. Goeddel, ed.); Gene Transfer Vectors For Mammalian Cells (J. H. Miller and M. P. Calos eds., 1987, Cold Spring Harbor Laboratory); Immunochemical Methods In Cell And Molecular Biology (Mayer and Walker, eds., Academic Press, London, 1987); Handbook Of Experimental Immunology, Volumes I-IV (D. M. Weir and C. C. Blackwell, eds., 1986); and Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986).
The present invention allows governing TALE/nucleic acid interactions in several directions by using arrays of particular RVDs in the repeat sequences of a TALE. The present invention allows to increase the specificity of a RVD array to one target compared to all other possible targets therefore reducing the off-target TALE/DNA interactions by using highly specific RVDs compared to natural RVDs.
New RVDs according to the present invention are selected from the group consisting of:

    
    
        II, TI, YI, PI, SI, CL, DL FL, GL, HL, IL, KL, LL, YL, MM, WY, PV, SW, XF for recognizing A, wherein X represents one amino acid residue selected from the group of A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, H, R and K;
        RE, QD for recognizing C
        NK, RK, ER, FR, GR, LR, QR, RR, VR, WK, YK for recognizing G
        PG, AP, LP, MP, VP for recognizing T
        CD, DD, FD, LD, TD, AE, EE, KE, QE, YE, CM, IM, NM, PM, QM, SM, YM, VM, FY, GY, KY, MY, NY, RY, SY, YY, HY for recognizing A or C
        RG, PH, VH, CK, FK, PK, QK, TK, DN, EN FN, GN, KN, PN, RN, TN, YN, WN, FQ, GQ, HQ, IQ, QQ, TQ, FT, LT, VT, PR, DS, SS, FV for recognizing A or G
        MG, PL, VP for recognizing A or T.
    
    


As a non-limiting illustrative example, RVD “IL” can be used as a highly specific or recognizing a nucleotide A in a nucleic acid target sequence. The present invention also allows to increase the flexibility of a RVD array therefore targeting more than one target or only a desired set of desired targets by locally decreasing the specificity of a RVD; as a non-limiting illustrative example, RVD “VT” can be used as a flexible RVD which is able to recognize A or G in a nucleic acid target sequence. The present invention also allows to increase or decrease the activity of a RVD array on a nucleic acid target sequence; as a non-limiting illustrative example, RVD “SW” can be used as a specific RVD for recognize a nucleotide A in a target sequence as A is the only nucleotide it recognizes but with less strength than a RVD “IL” which specifically and strongly recognizes a nucleotide A (Table 3; SEQ ID: 19-25). Several applications may result from the present invention; as a non-limiting example, several allelic polymorphisms (Single Nucleotide Polymorphisms or SNPs) differing by one or a few nucleotides substitutions at a particular genomic locus can be targeted by the same array of RVDs according to the present invention, by using more or less specific and/or more or less flexible and/or more or less active RVDs according to the present invention. A method that could result from the present invention allows the treatment of a particular genetic disease by constructing and administering one unique TALE derived protein or chimeric protein according to the invention to every subjects in need thereof, whatever SNPs profiles around said mutation responsible for genetic disease in these subjects. Hence, said method of the present invention avoids the need to construct and administer one personalized TALE derived protein or chimeric protein for each subject in need thereof that takes into account each SNP profile around the mutation to cure. As another non-limiting example, flexible and/or specific and/or active RVDs can be used to target a particular gene in different species whatever minor variations in gene sequence can exist in each targeted species.
I. TALE Derived Protein Comprising New RVD(s)
In a general aspect, the present invention relates to proteins that allow to efficiently target and/or process nucleic acids. In a particular aspect, the present invention relates to a protein comprising a repeat domain (also named TALE array) wherein the repeat domain comprises at least one repeat sequence (or repeat unit) derived from a Transcription Activator-Like Effector (TALE) wherein at least one repeat sequence comprises one or more Repeat Variable Diresidue region (RVD) according to the present invention which is responsible for the binding of one specific nucleotide in nucleic acid target sequence.
In an embodiment, said repeat domain comprises a plurality of repeat sequences derived from a TALE. In another embodiment, said repeat domain comprises a plurality of repeat sequences derived from a TALE and at least another repeat sequence not derived from a TALE. In another embodiment, said repeat domain contains a plurality of repeat sequences derived from a TALE and at least another repeat sequence partially derived from a TALE. In another embodiment, said repeat domain contains a plurality of repeat sequences partially derived from a TALE. In another embodiment, said repeat sequences partially derived from a TALE can be obtained using substitution matrix for sequence alignment proteins. Non-limiting examples of substitution matrix for sequence alignment proteins include, for example, BLOSUM (Yakubovskaya, Mejia et al. 2010) or PAM Matrices (Dayhoff, M. O., Schwartz, R. and Orcutt, B. C. 1978). As non-limiting illustrative examples, repeat sequences obtained using BLOSUM substitution matrix are given by SEQ ID NO: 6 to 8. In another embodiment, said repeat sequences partially derived from a TALE can be obtained using homologous protein structures. Non-limiting examples of homologous protein structures include, for example, MTERF1 (mitochondria transcription terminator1) (Henikoff and Henikoff 1992) or tetratricopeptide repeat (TPR)-like domain (Murakami, M. T. et al. 2010). Non-limiting illustrative examples of repeat sequences partially derived from MTERF1 structures are given by SEQ ID NO: 15 to 18. In another embodiment, said repeat sequences not derived (partially derived) from a TALE can be obtained by modifying, as non-limiting examples, loop and/or helices regions. Non-limiting illustrative examples are given by SEQ ID NO: 1-5 and 9-14.
In a preferred embodiment, said repeat domain contains between 8 and 30 repeat sequences derived from a TALE, more preferably between 8 and 20, again more preferably 15. More preferably, repeat sequences of a TALE DNA binding domain according to the present invention comprising 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 repeat sequences.
In another embodiment, said repeat sequences (or repeat units) are made of 30 to 42 amino acids, more preferably 33 to 35 amino acids, again more preferably 33 or 34 wherein two critical amino acids located at positions 12 and 13, i.e. Repeat Variable-Diresidue (RVD), mediates the recognition of one nucleotide in said nucleic acid target sequence. In another embodiment, RVDs comprise any known amino acid residues in positions 12 and 13. In a preferred embodiment, RVDs comprise one amino acid residue from the group consisting of A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, H, R and K in position 12 according to amino acid one-letter code. In another preferred embodiment, RVDs comprise one amino acid residue from the group consisting of A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, H, R and K in position 13 according to amino acid one-letter code. In another embodiment, RVDs comprise a combination of amino acid residues A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, H, R and K according to amino acid one-letter code in positions 12 and 13 for recognizing nucleotides A, C, G and T in a nucleic acid target sequence. In a preferred embodiment, one or more RVD of repeat sequences is selected from the group consisting of:

    
    
        II, TI, YI, PI, SI, CL, DL FL, GL, HL, IL, KL, LL, YL, MM, WY, PV, SW, XF for recognizing A, wherein X represents one amino acid residue selected from the group consisting of A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, H, R and K;
        RE, QD for recognizing C
        NK, RK, ER, FR, GR, LR, QR, RR, VR, WK, YK for recognizing G
        PG, AP, LP, MP, VP for recognizing T
        CD, DD, FD, LD, TD, AE, EE, KE, QE, YE, CM, IM, NM, PM, QM, SM, YM, VM, FY, GY, KY, MY, NY, RY, SY, YY, HY for recognizing A or C
        RG, PH, VH, CK, FK, PK, QK, TK, DN, EN FN, GN, KN, PN, RN, TN, YN, WN, FQ, GQ, HQ, IQ, QQ, TQ, FT, LT, VT, PR, DS, SS, FV for recognizing A or G
        MG, PL, VP for recognizing A or T
    
    


More particularly, the present invention relates to a Transcription Activator-Like Effector (TALE) DNA binding domain specific for a nucleic acid target sequence comprising a plurality of TALE repeat sequences (also named repeat units) containing each one a Repeat Variable Diresidue region (RVD) as described above which is responsible for the binding of one specific nucleotide pair in said nucleic acid target sequence. In a particular embodiment, further amino acid substitutions in positions 11 and 14 of one or several repeat sequences of said Transcription Activator-Like Effector (TALE) DNA binding domain specific for a nucleic acid target sequence can be present. Repeat sequences according to the invention can comprise a mutation on residue 14. In another embodiment, repeat sequences comprise one amino acid residue from the group consisting of A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, H, R and K in position 14 according to amino acid one-letter code for recognizing nucleotides A, C, G and T. In another embodiment, RVDs comprise a combination of amino acid residues A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, H, R and K according to amino acid one-letter code in positions 12, 13 and 14 for recognizing nucleotides A, C, G and T in a nucleic acid target sequence. In other words, the scope of the present invention encompasses Repeat Variable Triresidue responsible for the binding of one nucleotide in a nucleic acid target sequence.
In a further embodiment, repeat sequences comprise a mutation on residue 11 of the repeat sequence and can comprise one amino acid residue from the group consisting of A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, H, R and K in position 11 according to amino acid one-letter code. In another embodiment, RVDs comprise a combination of amino acid residues A, G, V, L, I, M, 5, T, C, P, D, E, F, Y, W, Q, N, H, R and K according to amino acid one-letter code in positions 11, 12, 13 and 14 for recognizing nucleotides A, C, G and T in a nucleic acid target sequence. In other words, the present invention encompasses Repeat Variable Quadriresidue responsible for the binding of one nucleotide in a nucleic acid target sequence. In another embodiment, repeat sequences comprise a combination of amino acid residues A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, H, R and K according to amino acid one-letter code in positions 11, 12 and 14, in positions 11, 13 and 14 or in positions 11, 12 and 13 for recognizing nucleotides A, C, G and T in a nucleic acid target sequence. In another embodiment, repeat sequences comprise a combination of amino acid residues A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, H, R and K according to amino acid one-letter code in positions 12 and 14, 13 and 14, 11 and 14, 11 and 13 or in positions 11 and 12 for recognizing nucleotides A, C, G and T in a nucleic acid target sequence.
In another embodiment, the combination of amino acid residues present in positions 12 and 13 of a RVD “n” influences the combination of amino acid residues present in positions 12 and 13 of a RVD “n−1” or “n+1” in the repeat domain of the polypeptides of the present invention. In another embodiment, further amino acid substitutions in positions 11 and 14 of a RVD “n” can influence the combination of amino acid residues present in positions 12 and 13 of a RVD “n−1” or “n+1” in the repeat domain of the polypeptides of the present invention.
In preferred particular embodiment, repeat domain of the polypeptides of the present invention contains specific pairs of RVDs for recognizing specific pairs of nucleotides A, C, G and T in a nucleic acid target sequence. In another preferred embodiment, said specific pairs of RVDs for recognizing specific pairs of nucleotides A, C, G and T in a nucleic acid target sequence are different from the two RVDs able to individually recognize nucleotides composing said pair of nucleotides; in other words, said pairs of RVDs contain combinations of amino acid residues in positions 12 and 13 that are different from the combinations of amino acid residues present in positions 12 and 13 of the individual RVDs. As a non-limiting example, in the polypeptides of the present invention a pair of RVDs for recognizing nucleotides sequence “AG” can comprise amino acid residues in positions 12 and 13 different from pairs “TL-VT” or “VT-VT” that would result from the teaching of individual RVDs recognizing successive nucleotides A and G (Table 3; SEQ ID: 19-25). In another embodiment, further amino acid substitutions in positions 11 and 14 of one or two RVDs of a specific pair of RVDs for recognizing specific pairs of nucleotides A, C, G and T in a nucleic acid target sequence can be present.
In another particular embodiment, repeat domain of the polypeptides of the present invention contains specific triplets of RVDs for recognizing specific triplets of nucleotides A, C, G and T in a nucleic acid target sequence. In another preferred embodiment, said specific triplets of RVDs for recognizing specific triplets of nucleotides A, C, G and T in a nucleic acid target sequence are different from the three RVDs able to individually recognize nucleotides composing said triplet of nucleotides; in other words, said triplets of RVDs contain combinations of amino acid residues in positions 12 and 13 that are different from the combinations of amino acid residues present in positions 12 and 13 of the individual RVDs. As a non-limiting example, in the polypeptides of the present invention a triplet of RVDs for recognizing nucleotides sequence “AGG” can comprise amino acid residues in positions 12 and 13 different from triplets “IL-VT-VT” or “VT-VT-VT” that would result from the teaching of individual RVDs recognizing successive nucleotides A and G (Table 3; SEQ ID: 19-25). In another embodiment, further amino acid substitutions in positions 11 and 14 of one or two or three RVDs of a specific triplet of RVDs for recognizing specific triplets of nucleotides A, C, G and T in a nucleic acid target sequence can be present.
II. Chimeric TALE Derived Protein Comprising New RVD(s)
In another embodiment the present invention relates to a chimeric protein derived from a TALE corresponding to a fusion between a TALE DNA binding domain as mentioned above and an additional protein domain to process the nucleic acid within or adjacent to the specific nucleic acid target sequence. In other words, said polypeptide of the present invention is a chimeric protein derived from a TALE comprising:

    (a) A Transcription Activator-Like Effector (TALE) DNA binding domain specific for a nucleic acid target sequence comprising a plurality of TALE repeat sequences comprising each one a Repeat Variable Diresidue region (RVD) which is responsible for the binding of one specific nucleotide in said nucleic acid target sequence; wherein one or more RVD is selected from the group consisting of:
    
        II, TI, YI, PI, SI, CL, DL FL, GL, HL, IL, KL, LL, YL, MM, WY, PV, SW, XF for recognizing A, wherein X represents one amino acid residue selected from the group consisting of A, G, V, L, I, M, 5, T, C, P, D, E, F, Y, W, Q, N, H, R and K;
        RE, QD for recognizing C
        NK, RK, ER, FR, GR, LR, QR, RR, VR, WK, YK for recognizing G
        PG, AP, LP, MP, VP for recognizing T
        CD, DD, FD, LD, TD, AE, EE, KE, QE, YE, CM, IM, NM, PM, QM, SM, YM, VM, FY, GY, KY, MY, NY, RY, SY, YY, HY for recognizing A or C
        RG, PH, VH, CK, FK, PK QK TK, DN, EN FN, GN, KN, PN, RN, TN, YN, WN, FQ, GQ, HQ, IQ, QQ, TQ, FT, LT, VT, PR, DS, SS, FV for recognizing A or G
        MG, PL, VP for recognizing A or T
    
    
    (b) An additional domain to process the nucleic acid within or adjacent to the specific nucleic acid target sequence.


In another embodiment, said chimeric protein according to the present invention can comprise at least one peptidic linker to fuse said TALE DNA binding domain and said additional protein domain processing the nucleic acid. In a preferred embodiment, said peptidic linker is flexible. In another preferred embodiment, said peptidic linker is structured.
In a particular embodiment, the additional protein domain of the chimeric protein of the present invention can be a transcription activator or repressor (i.e. a transcription regulator), or a protein that interacts with or modifies other proteins implicated in DNA processing. Non-limiting examples of DNA processing activities of said chimeric protein of the present invention include, for example, creating or modifying epigenetic regulatory elements, making site-specific insertions, deletions, or repairs in DNA, controlling gene expression, and modifying chromatin structure.
In another particular embodiment, said additional protein domain has catalytic activity selected from the group consisting of nuclease activity, polymerase activity, kinase activity, phosphatase activity, methylase activity, topoisomerase activity, integrase activity, transposase activity, ligase activity, helicase activity, recombinase activity. In a preferred embodiment, said additional protein domain is a nuclease, preferably an endonuclease; in another preferred embodiment, said protein domain is an exonuclease.
When comprising an endonuclease, said chimeric protein of the present invention derived from a TALE is a TALE-nuclease; in other words, in the scope of the present invention is a TALE-nuclease comprising:

    (a) A Transcription Activator-Like Effector (TALE) DNA binding domain specific for a nucleic acid target sequence comprising a plurality of TALE repeat sequences comprising each one a Repeat Variable Diresidue region (RVD) which is responsible for the binding of one specific nucleotide in said nucleic acid target sequence, wherein one or more RVDs is selected from the group consisting of:
    
        II, TI, YI, PI, SI, CL, DL FL, GL, HL, IL, KL, LL, YL, MM, WY, PV, SW, XF for recognizing A, wherein X represents one amino acid residue selected from the group consisting of A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, H, R and K;
        RE, QD for recognizing C
        NK, RK, ER, FR, GR, LR, QR, RR, VR, WK, YK for recognizing G
        PG, AP, LP, MP, VP for recognizing T
        CD, DD, FD, LD, TD, AE, EE, KE, QE, YE, CM, IM, NM, PM, QM, SM, YM, VM, FY, GY, KY, MY, NY, RY, SY, YY, HY for recognizing A or C
        RG, PH, VH, CK, FK, PK, QK, TK, DN, EN, FN, GN, KN, PN, RN, TN, YN, WN, FQ, GQ, HQ, IQ, QQ, TQ, FT, LT, VT, PR, DS, SS, FV for recognizing A or G
        MG, PL, VP for recognizing A or T;
    
    
    (b) An endonuclease domain to cleave the nucleic acid within or adjacent to the specific nucleic acid target sequence.


In another embodiment, further amino acid substitutions in positions 11 and 14 of one or several RVDs of said chimeric protein or TALE-nuclease according to the present invention can be present.
In a preferred embodiment, said TALE-nuclease according to the present invention can comprise at least one peptidic linker to fuse said TALE DNA binding domain and said endonuclease domain. In a preferred embodiment, said peptidic linker is flexible. In another preferred embodiment, said peptidic linker is structured.
Depending on the endonuclease domain that constitutes said TALE-nuclease according to the present invention, cleavage in the nucleic acid within or adjacent to the specific nucleic acid target sequence corresponds to either a double-stranded break or a single-stranded break.
As non limiting example, said endonuclease can be a type IIS FokI endonuclease domain or functional variant thereof which functions independently of the DNA binding domain and induces nucleic acid double-stranded cleavage as a dimer (Li, Wu et al. 1992; Kim, Cha et al. 1996). Amino acid sequence of FokI variants can be prepared by mutations in the DNA, which encodes the catalytic domain. Such variants include, for example, deletions from, or insertions or substitutions of, residues within the amino acid sequence. Any combination of deletion, insertion, and substitution may also be made to arrive at the final construct, provided that the final construct possesses the desired activity. Said nuclease domain of FokI variant according to the present invention comprises a fragment of a protein sequence having at least 80%, more preferably 90%, again more preferably 95% amino acid sequence identity with the protein sequence of FokI. In particular embodiment, a first and a second chimeric proteins can function respectively as monomer to act together as a dimer to process the nucleic acid within or adjacent to a specific nucleic acid target. As a non-limiting example, the two monomers can recognize different adjacent nucleic acid target sequences and the two protein domains constituting each chimeric protein derived from a TALE, function as subdomains that need to interact in order to process the nucleic acid within or adjacent to said specific nucleic acid target sequence.
In another particular embodiment, said chimeric protein is a monomeric TALE-nuclease that does not require dimerization for specific recognition and cleavage. As non limiting example, such monomeric TALE-nuclease comprises a TALE DNA binding domain fused to the catalytic domain of 1-Tevl or a variant thereof.
It is understood that RVDs, DNA binding domains, TALE-nucleases, chimeric protein and polypeptides according to the present invention can also comprise single or plural additional amino acid substitutions or amino acid insertion or amino acid deletion introduced by mutagenesis process well known in the art. Is also encompassed in the scope of the present invention variants, functional mutants and derivatives from RVDs, DNA binding domains, TALE-nucleases, chimeric protein and polypeptides according to the present invention. Are also encompassed in the scope of the present invention RVDs, DNA binding domains, TALE-nucleases, chimeric proteins and polypeptides which present a sequence with high percentage of identity or high percentage of homology with sequences of RVDs, DNA binding domains, TALE-nucleases, chimeric proteins and polypeptides according to the present invention, at nucleotidic or polypeptidic levels. By high percentage of identity or high percentage of homology it is intended 70%, more preferably 75%, more preferably 80%, more preferably 85%, more preferably 90%, more preferably 95, more preferably 97%, more preferably 99% or any integer comprised between 70% and 99%.
In another aspect of the present invention are polynucleotides encoding for or comprising a coding sequence for the polypeptides, TALE DNA binding domain, chimeric protein derived from a TALE and TALE-nuclease according to the present invention. Is also encompassed a vector comprising such polynucleotides.
Is also encompassed in the scope of the present invention a host cell which comprises a vector and/or a recombinant polynucleotide encoding for or comprising a coding sequence for the polypeptides, TALE DNA binding domain, chimeric protein derived from a TALE and TALE-nuclease according to the present invention.
Is also encompassed in the scope of the present invention a non-human transgenic animal comprising a vector and/or a recombinant polynucleotide encoding for or comprising a coding sequence for the polypeptides, TALE DNA binding domain, chimeric protein derived from a TALE and TALE-nuclease according to the present invention.
Is also encompassed in the scope of the present invention a transgenic plant comprising a vector and/or a recombinant polynucleotide encoding for or comprising a coding sequence for the polypeptides, TALE DNA binding domain, chimeric protein derived from a TALE and TALE-nuclease according to the present invention.
The present invention also relates to a kit comprising a polypeptide or a TALE DNA binding domain or a chimeric protein derived from a TALE or a TALE-nuclease according to the present invention or a vector and/or a recombinant polynucleotide encoding for or comprising a coding sequence for such recombinant molecules and instructions for use said kit.
The present invention also relates to a composition comprising a polypeptide or a TALE DNA binding domain or a chimeric protein derived from a TALE or a TALE-nuclease according to the present invention or a vector and/or a recombinant polynucleotide encoding for or comprising a coding sequence for such recombinant molecules and a carrier. More preferably, is a pharmaceutical composition comprising such recombinant molecules and a pharmaceutically active carrier. For purposes of therapy, the chimeric protein according to the present invention and a pharmaceutically acceptable excipient are administered in a therapeutically effective amount. Such a combination is said to be administered in a “therapeutically effective amount” if the amount administered is physiologically significant. An agent is physiologically significant if its presence results in a detectable change in the physiology of the recipient. In the present context, an agent is physiologically significant if its presence results in a decrease in the severity of one or more symptoms of the targeted disease and in a genome correction of the lesion or abnormality.
III. Methods
In another aspect, the present invention also relates to methods for use of protein comprising TALE domain according to the present invention for various applications ranging from targeted nucleic acid cleavage to targeted gene regulation.
More particularly, the present invention relates to a method for binding a nucleic acid target sequence comprising:

    (a) Selecting a nucleic acid target sequence;
    (b) Engineering a protein comprising at least one Transcription Activator-Like Effector (TALE) domain wherein said TALE domain comprises a plurality of TALE repeat sequences comprising each one a Repeat Variable Diresidue region (RVD) which is responsible for the binding of one specific nucleotide in the nucleic acid target sequence, wherein one or more RVD is selected from the group consisting of:
    
        II, TI, YI, PI, SI, CL, DL, FL, GL, HL, IL, KL, LL, YL, MM, WY, PV, SW, XF for recognizing A, wherein X represents one amino acid residue selected from the group consisting of A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, H, R and K;
        RE, QD for recognizing C
        NK, RK, ER, FR, GR, LR, QR, RR, VR, WK, YK for recognizing G
        PG, AP, LP, MP, VP for recognizing T
        CD, DD, FD, LD, TD, AE, EE, KE, QE, YE, CM, IM, NM, PM, QM, SM, YM, VM, FY, GY, KY, MY, NY, RY, SY, YY, HY for recognizing A or C
        RG, PH, VH, CK, FK, PK, QK, TK, DN, EN, FN, GN, KN, PN, RN, TN, YN, WN, FQ, GQ, HQ, IQ, QQ, TQ, FT, LT, VT, PR, DS, SS, FV for recognizing A or G
        MG, PL, VP for recognizing A or T
    
    
    (c) Contacting said engineered protein with said nucleic acid target sequence such that the engineered protein binds to said nucleic acid target sequence.


In particular embodiment, the present invention relates to a method for processing a genetic material in a cell comprising:

    (a) Providing a cell comprising a nucleic acid target sequence;
    (b) Engineering a protein comprising at least one Transcription Activator-Like Effector (TALE) domain wherein said TALE domain comprises a plurality of TALE repeat sequences comprising each one a Repeat Variable Diresidue region (RVD) which is responsible for the binding of one specific nucleotide in the nucleic acid target sequence, wherein one or more RVD is selected from the group consisting of:
    
        II, TI, YI, PI, SI, CL, DL FL, GL, HL, IL, KL, LL, YL, MM, WY, PV, SW, XF for recognizing A, wherein X represents one amino acid residue selected from the group consisting of A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, H, R and K;
        RE, QD for recognizing C
        NK, RK, ER, FR, GR, LR, OR, RR, VR, WK, YK for recognizing G
        PG, AP, LP, MP, VP for recognizing T
        CD, DD, FD, LD, TD, AE, EE, KE, QE, YE, CM, IM, NM, PM, QM, SM, YM, VM, FY, GY, KY, MY, NY, RY, SY, YY, HY for recognizing A or C
        RG, PH, VH, CK, FK, PK, QK, TK, DN, EN, FN, GN, KN, PN, RN, TN, YN, WN, FQ, GQ, HQ, IQ, QQ, TQ, FT, LT, VT, PR, DS, SS, FV for recognizing A or G
        MG, PL, VP for recognizing A or T
    
    
    (c) Introducing said protein into a cell.


The term “processing” as used herein means that the sequence is considered modified simply by the binding of the protein. Any nucleic acid target sequence can be processed by the present methods. For example, the nucleic acid target sequence can be chromosomal, mitochondrial or chloroplast sequences.
In a more particular embodiment, said engineered protein of step (b) is a chimeric protein as described above further comprising an additional protein domain fused to the TALE domain. In a particular embodiment, the additional protein domain of the chimeric protein of the present invention can be a transcription activator or repressor (i.e. a transcription regulator), or a protein that interacts with or modifies other proteins implicated in DNA processing. Non-limiting examples of DNA processing activities of said chimeric protein of the present invention include, for example, creating or modifying epigenetic regulatory elements, making site-specific insertions, deletions, or repairs in DNA, controlling gene expression, and modifying chromatin structure.
In another embodiment, said additional protein domain has catalytic activity selected from the group consisting of nuclease activity, polymerase activity, kinase activity, phosphatase activity, methylase activity, topoisomerase activity, integrase activity, transposase activity, ligase activity, helicase activity, recombinase activity. In a preferred embodiment, said protein domain is a nuclease, preferably an endonuclease; in another preferred embodiment, said protein domain is an exonuclease.
The present invention more particularly relates to a method for modifying the genetic material of a cell within or adjacent to a nucleic acid target sequence. The double strand breaks caused by endonucleases are commonly repaired through non-homologous end joining (NHEJ). NHEJ comprises at least two different processes. Mechanisms involve rejoining of what remains of the two DNA ends through direct re-ligation (Critchlow and Jackson 1998) or via the so-called microhomology-mediated end joining (Ma, Kim et al. 2003). Repair via non-homologous end joining (NHEJ) often results in small insertions or deletions and can be used for the creation of specific gene knockouts. The present invention relates to a method for modifying the genetic material in a cell within or adjacent to a nucleic acid target sequence by using chimeric protein, preferably a TALE-nuclease according to the present invention that allows nucleic acid cleavage that will lead to the loss of genetic information and any NHEJ pathway will produce targeted mutagenesis. In a preferred embodiment, the present invention related to a method for modifying the genetic material of a cell within or adjacent to a nucleic acid target sequence by generating at least one nucleic acid cleavage and a loss of genetic information around said nucleic acid target sequence thus preventing any scarless re-ligation by NHEJ. Said modification may be a deletion of the genetic material, insertion of nucleotides in the genetic material or a combination of both deletion and insertion of nucleotides.
The present invention also relates to a method for modifying nucleic acid target sequence further comprising the step of expressing an additional catalytic domain into a host cell. In a more preferred embodiment, the present invention relates to a method to increase mutagenesis wherein said additional catalytic domain is a DNA end-processing enzyme. Non limiting examples of DNA end-processing enzymes include 5-3′ exonucleases, 3-5′ exonucleases, 5-3′ alkaline exonucleases, 5′ flap endonucleases, helicases, hosphatase, hydrolases and template-independent DNA polymerases. Non limiting examples of such catalytic domain comprise of a protein domain or catalytically active derivate of the protein domain selected from the group consisting of hExoI (EXO1_HUMAN), Yeast ExoI (EXO1_YEAST), E. coli ExoI, Human TREX2, Mouse TREX1, Human TREX1, Bovine TREX1, Rat TREX1, TdT (terminal deoxynucleotidyl transferase) Human DNA2, Yeast DNA2 (DNA2_YEAST). In a preferred embodiment, said additional catalytic domain has a 3′-5′-exonuclease activity, and in a more preferred embodiment, said additional catalytic domain has TREX exonuclease activity, more preferably TREX2 activity. In another preferred embodiment, said catalytic domain is encoded by a single chain TREX polypeptide. Said additional catalytic domain may be fused to the chimeric protein according to the invention optionally by a peptide linker. It has been found that the coupling of the enzyme TREX2 with an endonuclease such as a TALE-nuclease ensures high frequency of targeted mutagenesis (WO2012/058458)
In a preferred embodiment, the present invention relates to a method for modifying the genetic material of a cell comprising:

    (a) Providing a cell comprising a nucleic acid target sequence;
    (b) Introducing a protein comprising at least:
    
        (i) A Transcription Activator-Like Effector (TALE) DNA binding domain specific for a nucleic acid target sequence comprising a plurality of TALE repeat sequences comprising each one a Repeat Variable Diresidue region (RVD) which is responsible for the binding of one specific nucleotide in said nucleic acid target sequence and wherein said TALE DNA binding domain comprises one or more RVDs selected from the group consisting of:
        II, TI, YI, PI, SI, CL, DL FL, GL, HL, IL, KL, LL, YL, MM, WY, PV, SW, XF for recognizing A, wherein X represents one amino acid residue selected from the group consisting of A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, H, R and K;
        RE, QD for recognizing C
        NK, RK, ER, FR, GR, LR, QR, RR, VR, WK, YK for recognizing G
        PG, AP, LP, MP, VP for recognizing T
        CD, DD, FD, LD, TD, AE, EE, KE, QE, YE, CM, IM, NM, PM, QM, SM, YM, VM, FY, GY, KY, MY, NY, RY, SY, YY, HY for recognizing A or C
        RG, PH, VH, CK, FK, PK, QK, TK, DN, EN, FN, GN, KN, PN, RN, TN, YN, WN, FQ, GQ, HQ, IQ, QQ, TQ, FT, LT, VT, PR, DS, SS, FV for recognizing A or G
        MG, PL, VP for recognizing A or T
    
    
    (ii) An endonuclease,
    (c) Inducing the expression of protein of (b);
    (d) Selecting the cells in which cleavage within or adjacent to the specific nucleic acid target sequence has occurred.


In another embodiment, cells in which said protein has been introduced is selected by a selection method well-known in the art. As non-limiting example, said protein or chimeric protein can be introduced as a transgene encoded by a plasmidic vector; said plasmidic vector contains a selection marker which allows to identify and/or select cells which received said vector. Said protein expression can be induced in selected cells and said TALE domain of the protein bind nucleic acid target sequence in selected cells, thereby obtaining cells in which TALE domain binds a specific nucleic acid target sequence. The methods of the invention involve introducing a polynucleotide encoding engineered protein or chimeric protein into a cell. Vectors comprising targeting nucleic acid and/or nucleic acid encoding engineered protein or chimeric protein according to the present invention can be introduced into a cell by a variety of methods (e.g., injection, direct uptake, projectile bombardment, liposomes, electroporation). Engineered protein or chimeric proteins according to the present invention can be stably or transiently expressed into cells using expression vectors. Techniques of expression in eukaryotic cells are well known to those in the art. (See Current Protocols in Human Genetics: Chapter 12 “Vectors For Gene Therapy” & Chapter 13 “Delivery Systems for Gene Therapy”). The protein may be synthesized in situ in the cell as a result of the introduction of polynucleotide encoding protein into the cell. Alternatively, the protein could be produced outside the cell and then introduced thereto by well known method of the art.
Cells in which a cleavage-induced mutagenesis event, i.e. a mutagenesis event consecutive to an NHEJ event, has occurred can be identified and/or selected by well-known method in the art. As a non-limiting example, deep-sequencing analysis can be generated from the targeted cell genome around the targeted locus. Insertion/deletion events (mutagenesis events) can be therefore detected. As another non-limiting example, assays based on T7 endonuclease that recognizes non-perfectly matched DNA can be used, to quantify from a locus specific PCR on genomic DNA from provided cells, mismatches between reannealed DNA strands coming from cleaved/non-cleaved DNA molecules.
Endonucleolytic breaks are known to stimulate the rate of homologous recombination. Therefore, in another embodiment, the present invention relates to a method for inducing homologous gene targeting in the nucleic acid target sequence further comprising introducing into the cell an exogeneous nucleic acid comprising at least a sequence homologous to a portion of the nucleic acid target sequence, such that homologous recombination occurs between the target nucleic acid sequence and the exogeneous nucleic acid. In other words, following cleavage of the nucleic acid target sequence, a homologous recombination event is stimulated between the nucleic acid target sequence and the exogenous nucleic acid. By nucleic acid homologous sequence it is meant a nucleic acid sequence with enough identity to another one to lead to homologous recombination between sequences, more particularly having at least 80% identity, preferably at least 90% identity and more preferably at least 95%, and even more preferably 98% identity.
In another embodiment, said exogenous nucleic acid comprises two sequences homologous to portions or adjacent portions of said nucleic acid target sequence flanking a sequence to introduce in the nucleic acid target sequence. Preferably, said exogenous nucleic acid comprises first and second portions which are homologous to region 5′ and 3′ of the nucleic acid target, respectively. In another embodiment, said exogenous sequence allows introducing new genetic material into a cell. Said exogenous nucleic acid in this embodiment also comprises a third portion positioned between the first and the second portion which comprises no homology with the regions 5′ and 3′ of the nucleic acid target sequence. Said new genetic material introduced into a cell can confer a selective or a commercial advantage to said cell. In another embodiment, said exogenous sequence allows to replace genetic material into a cell. In another embodiment, said exogenous sequence allows to repair genetic material into a cell.
Preferably, homologous sequences of at least 50 bp, preferably more than 100 bp and more preferably more than 200 bp are used within said donor matrix. Therefore, the exogenous nucleic acid is preferably from 200 bp to 6000 bp, more preferably from 1000 bp to 2000 bp. Indeed, shared nucleic acid homologies are located in regions flanking upstream and downstream the site of the cleavage and the nucleic acid sequence to be introduced should be located between the two arms.
In particular embodiments, said exogenous nucleic acid can comprise a positive selection marker between the two homology arms and eventually a negative selection marker upstream of the first homology arm or downstream of the second homology arm. The marker(s) allow(s) the selection of the cells having inserted the sequence of interest by homologous recombination at the target site. Depending on the location of the targeted genome sequence wherein break event has occurred, such exogenous nucleic acid can be used to knock-out a gene, e.g. when exogenous nucleic acid is located within the open reading frame of said gene, or to introduce new sequences or genes of interest. Sequence insertions by using such exogenous nucleic acid can be used to modify a targeted existing gene, by correction or replacement of said gene (allele swap as a non-limiting example), or to up- or down-regulate the expression of the targeted gene (promoter swap as non-limiting example), said targeted gene correction or replacement. In a particular embodiment, the exogenous nucleic acid is included in a vector encoding the TALE-derived protein or chimeric protein or alternatively, in a different vector. In another particular embodiment, the exogenous nucleic acid is a single- or double stranded oligonucleotide.
Cells in which a homologous recombination event has occurred can be selected by methods well-known in the art. As a non-limiting example, PCR analysis using one oligonucleotide matching within the exogenous nucleic acid sequence and one oligonucleotide matching the genomic nucleic acid of cells outside said exogenous nucleic acid but close to the targeted locus can be performed. Therefore, cells in which methods of the invention allowed a mutagenesis event or a homologous recombination event to occur can be selected.
In another embodiment, said exogenous sequence to be introduced into a cell can be optimized in order to be not cleavable by the protein used to generate the initial double-stranded break. In other words, in the case where a nucleic acid target sequence has to be corrected by replacement consecutively to a double-stranded break generated by a protein or a chimeric protein according to the present invention, exogenous replacement sequence can be modified in order to be not cleavable again by the original protein or chimeric protein. Said modifications include as non-limiting example silent mutations when targeted sequence is in a coding sequence of a gene or mutations when targeted sequence is in a non-coding sequence of a gene.
Another aspect of the invention is a method for producing one Transcription Activator-Like Effector (TALE) domain comprising:

    (a) Determining a nucleic acid target sequence;
    (b) Synthesizing a repeat sequence domain specific for a nucleic acid target sequence comprising a plurality of TALE repeat sequences comprising each one a Repeat Variable Diresidue region (RVD) which is responsible for the binding of one specific nucleotide in said nucleic acid target sequence, wherein one or more RVD is selected from the group consisting of:
    
        II, TI, YI, PI, SI, CL, DL FL, GL, HL, IL, KL, LL, YL, MM, WY, PV, SW, XF for recognizing A, wherein X represents one amino acid residue selected from the group consisting of A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, H, R and K;
        RE, QD for recognizing C;
        NK, RK, ER, FR, GR, LR, QR, RR, VR, WK, YK for recognizing G;
        PG, AP, LP, MP, VP for recognizing T;
        CD, DD, FD, LD, TD, AE, EE, KE, QE, YE, CM, IM, NM, PM, QM, SM, YM, VM, FY, GY, KY, MY, NY, RY, SY, YY, HY for recognizing A or C;
        RG, PH, VH, CK, FK, PK, QK, TK, DN, EN, FN, GN, KN, PN, RN, TN, YN, WN, FQ, GQ, HQ, IQ, QQ, TQ, FT, LT, VT, PR, DS, SS, FV for recognizing A or G;
        MG, PL, VP for recognizing A or T.
    
    


In a particular embodiment, the present invention relates to a method for producing a chimeric protein further comprising:

    (c) Providing an additional protein domain to process the nucleic acid within or adjacent to the specific nucleic acid target sequence;
    (d) Optionally designing a peptidic linker to link TALE domain with said additional protein domain;
    (e) Assembling said chimeric protein.


The scope of the present invention also encompasses a chimeric protein obtainable by a method comprising at least the steps of:

    (a) Determining a nucleic acid target sequence;
    (b) Synthesizing a repeat sequence domain specific for a nucleic acid target sequence comprising a plurality of TALE repeat sequences comprising each one a Repeat Variable Diresidue region (RVD) which is responsible for the binding of one specific nucleotide in said nucleic acid target sequence, wherein one or more RVD is selected from the group consisting of:
    
        II, TI, VI, PI, SI, CL, DL, FL, GL, HL, IL, KL, LL, YL, MM, WY, PV, SW, XF for recognizing A, wherein X represents one amino acid residue selected from the group consisting of A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, H, R and K;
        RE, QD for recognizing C
        NK, RK, ER, FR, GR, LR, QR, RR, VR, WK, YK for recognizing G
        PG, AP, LP, MP, VP for recognizing T
        CD, DD, FD, LD, TD, AE, EE, KE, QE, YE, CM, IM, NM, PM, QM, SM, YM, VM, FY, GY, KY, MY, NY, RY, SY, YY, HY for recognizing A or C
        RG, PH, VH, CK, FK, PK, QK, TK, DN, EN FN, GN, KN, PN, RN, TN, YN, WN, FQ, GQ, HQ, IQ, QQ, TQ, FT, LT, VT, PR, DS, SS, FV for recognizing A or G
        MG, PL, VP for recognizing A or T
    
    
    (c) Providing an additional protein domain to process the nucleic acid within or adjacent to the specific nucleic acid target sequence;
    (d) Optionally designing a peptidic linker to link polypeptides obtained in b) and c);
    (e) Assembling said chimeric protein;
    (f) Testing the activity of said chimeric protein.


In a further embodiment, synthesis step b) can be done using a solid support method composed of consecutive restriction/ligation/washing steps as shown in FIG. 1 and examples section; step c) can be done by cloning said protein domain of interest into a plasmidic vector; in the case where said chimeric protein according to the invention is a TALE-nuclease, as non-limiting example, said protein domain can be cloned together in a same vector with chosen peptidic linker and eventual additional N and C terminal backbones for a RVD. Assembling step e) can be done by cloning repeat sequence domain of step b) in the vector resulting from step e). Testing step f) can be done, in the case where said chimeric protein is a TALE-Nuclease as a non-limiting example, in yeast by using a yeast target reporter plasmid containing the nucleic acid target sequence as previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006). The activity of said TALE-nuclease can be tested at 30° C. and 37° C. in a yeast SSA assay previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006)
In another embodiment, the cell targeted or modified by the methods of the present invention is a eukaryotic cell preferably a mammalian cell, a plant cell or an algal cell.
In another embodiment, the nucleic acid sequence targeted or modified by the methods of the present invention is a chromosomal sequence or an episomal sequence. In another embodiment, said sequence is an organelle sequence.
The present invention also related to a method for generating a plant comprising providing a plant cell comprising a nucleic acid target sequence into which it is desired to introduce a genetic modification; generating a cleavage within or adjacent to the nucleic acid target sequence by introducing a chimeric protein such as a TALE-nuclease according to the present invention; and generating a plant from the cell or progeny thereof, in which cleavage has occurred. Progeny includes descendants of a particular plant or plant line. In a particular embodiment, the method for generating a plant further comprises introducing an exogenous nucleic acid as desired. Said exogenous nucleic acid comprises a sequence homologous to at least a portion of the nucleic acid target sequence, such that homologous recombination occurs between said exogenous nucleic acid and the nucleic acid target sequence in the cell or progeny thereof. Plant cells produced using methods can be grown to generate plants having in their genome a modified nucleic acid target sequence. Seeds from such plants can be used to generate plants having a phenotype such as, for example, an altered growth characteristic, altered appearance, or altered compositions with respect to unmodified plants.
The polypeptides of the invention are useful to engineer genomes and to reprogram cells, especially induced Pluripotent Stem cells (iPS) and embryonic stem (ES) cells, preferably non human ES cells.
Other Definitions


    
    
        Amino acid residues in a polypeptide sequence are designated herein according to the one-letter code, in which, for example, Q means Gln or Glutamine residue, R means Arg or Arginine residue and D means Asp or Aspartic acid residue.
        Amino acid substitution means the replacement of one amino acid residue with another, for instance the replacement of an Arginine residue with a Glutamine residue in a peptide sequence is an amino acid substitution.
        DNA or nucleic acid processing activity refers to a particular/given enzymatic activity of a protein domain comprised in a chimeric protein or a polypeptide according to the invention such as in the expression “an additional protein domain to process the nucleic acid within or adjacent to the specific nucleic acid target sequence”. Said DNA or nucleic acid processing activity can refer to a cleavage activity, either a cleavase activity either a nickase activity, more broadly a nuclease activity but also a polymerase activity, a kinase activity, a phosphatase activity, a methylase activity, a topoisomerase activity, an integrase activity, a transposase activity, a ligase, a helicase or recombinase activity as non-limiting examples.
        Nucleotides are designated as follows: one-letter code is used for designating the base of a nucleoside: a is adenine, t is thymine, c is cytosine, and g is guanine. For the degenerated nucleotides, r represents g or a (purine nucleotides), k represents g or t, s represents g or c, w represents a or t, m represents a or c, y represents t or c (pyrimidine nucleotides), d represents g, a or t, v represents g, a or c, b represents g, t or c, h represents a, t or c, and n represents g, a, t or c.
        by “peptide linker” or “peptidic linker” it is intended to mean a peptide sequence which allows the connection of different monomers or different parts comprised in a fusion protein such as between a TALE DNA binding domain and a protein domain in a chimeric protein or a polypeptide according to the present invention and which allows the adoption of a correct conformation for said chimeric protein activity and/or specificity. Peptide linkers can be of various sizes, from 3 amino acids to 50 amino acids as a non limiting indicative range. Peptide linkers can also be qualified as structured or unstructured. Peptide linkers can be qualified as active linkers when they comprise active domains that are able to change their structural conformation under appropriate stimulation.
        by “subdomain” or “domain” it is intended a protein subdomain or a protein part that interacts with another protein subdomain or protein part to form an active entity and/or a catalytic active entity bearing nucleic acid or DNA processing activity of said chimeric protein or polypeptide according to the invention.
        by “DNA target”, “DNA target sequence”, “target DNA sequence”, “nucleic acid target sequence”, “target nucleic acid sequence”, “target sequence”, or “processing site” is intended a polynucleotide sequence that can be processed by a TALE derived protein or chimeric protein according to the present invention. These terms refer to a specific nucleic acid location, preferably a genomic location in a cell, but also a portion of genetic material that can exist independently to the main body of genetic material such as plasmids, episomes, virus, transposons or in organelles such as mitochondria or chloroplasts as non-limiting examples. The nucleic acid target sequence is defined by the 5′ to 3′ sequence of one strand of said target, as indicated for SEQ ID NO: 62-77 in table 2 and SES ID NO: 94-109 in table 5 as a non-limiting example.
        Adjacent is used to distinguish between 1) the nucleic acid sequence recognized and bound by a set of specific RVDs comprised in the TALE DNA binding domain of a polypeptide or a chimeric protein according to the present invention and 2) the nucleic acid target sequence to be processed by said polypeptide or chimeric protein according to the invention, said nucleic sequences 1) and 2) being adjacent.
        By “delivery vector” or “delivery vectors” is intended any delivery vector which can be used in the present invention to put into cell contact (i.e. “contacting”) or deliver inside cells or subcellular compartments agents/chemicals and molecules (proteins or nucleic acids) needed in the present invention. It includes, but is not limited to liposomal delivery vectors, viral delivery vectors, drug delivery vectors, chemical carriers, polymeric carriers, lipoplexes, polyplexes, dendrimers, microbubbles (ultrasound contrast agents), nanoparticles, emulsions or other appropriate transfer vectors. These delivery vectors allow delivery of molecules, chemicals, macromolecules (genes, proteins), or other vectors such as plasmids, peptides developed by Diatos. In these cases, delivery vectors are molecule carriers. By “delivery vector” or “delivery vectors” is also intended delivery methods to perform transfection.
        The terms “vector” or “vectors” refer to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. A “vector” in the present invention includes, but is not limited to, a viral vector, a plasmid, a RNA vector or a linear or circular DNA or RNA molecule which may consist of a chromosomal, non chromosomal, semi-synthetic or synthetic nucleic acids. Preferred vectors are those capable of autonomous replication (episomal vector) and/or expression of nucleic acids to which they are linked (expression vectors). Large numbers of suitable vectors are known to those of skill in the art and commercially available.
    
    


Viral vectors include retrovirus, adenovirus, parvovirus (e.g. adenoassociated viruses), coronavirus, negative strand RNA viruses such as orthomyxovirus (e.g., influenza virus), rhabdovirus (e.g., rabies and vesicular stomatitis virus), paramyxovirus (e.g. measles and Sendai), positive strand RNA viruses such as picornavirus and alphavirus, and double-stranded DNA viruses including adenovirus, herpesvirus (e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomegalovirus), and poxvirus (e.g., vaccinia, fowlpox and canarypox). Other viruses include Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, and hepatitis virus, for example. Examples of retroviruses include: avian leukosis-sarcoma, mammalian C-type, B-type viruses, D type viruses, HTLV-BLV group, lentivirus, spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, In Fundamental Virology, Third Edition, B. N. Fields, et al., Eds., Lippincott-Raven Publishers, Philadelphia, 1996).
By “lentiviral vector” is meant HIV-Based lentiviral vectors that are very promising for gene delivery because of their relatively large packaging capacity, reduced immunogenicity and their ability to stably transduce with high efficiency a large range of different cell types. Lentiviral vectors are usually generated following transient transfection of three (packaging, envelope and transfer) or more plasmids into producer cells. Like HIV, lentiviral vectors enter the target cell through the interaction of viral surface glycoproteins with receptors on the cell surface. On entry, the viral RNA undergoes reverse transcription, which is mediated by the viral reverse transcriptase complex. The product of reverse transcription is a double-stranded linear viral DNA, which is the substrate for viral integration in the DNA of infected cells.
By “integrative lentiviral vectors (or LV)”, is meant such vectors as non limiting example, that are able to integrate the genome of a target cell.
At the opposite by “non integrative lentiviral vectors (or NILV)” is meant efficient gene delivery vectors that do not integrate the genome of a target cell through the action of the virus integrase.
One type of preferred vector is an episome, i.e., a nucleic acid capable of extra-chromosomal replication. Preferred vectors are those capable of autonomous replication and/or expression of nucleic acids to which they are linked. Vectors capable of directing the expression of genes to which they are operatively linked are referred to herein as “expression vectors. A vector according to the present invention comprises, but is not limited to, a YAC (yeast artificial chromosome), a BAC (bacterial artificial), a baculovirus vector, a phage, a phagemid, a cosmid, a viral vector, a plasmid, a RNA vector or a linear or circular DNA or RNA molecule which may consist of chromosomal, non chromosomal, semi-synthetic or synthetic DNA. In general, expression vectors of utility in recombinant DNA techniques are often in the form of “plasmids” which refer generally to circular double stranded DNA loops which, in their vector form are not bound to the chromosome. Large numbers of suitable vectors are known to those of skill in the art. Vectors can comprise selectable markers, for example: neomycin phosphotransferase, histidinol dehydrogenase, dihydrofolate reductase, hygromycin phosphotransferase, herpes simplex virus thymidine kinase, adenosine deaminase, glutamine synthetase, and hypoxanthine-guanine phosphoribosyl transferase for eukaryotic cell culture; TRP1 for S. cerevisiae; tetracyclin, rifampicin or ampicillin resistance in E. coli. Preferably said vectors are expression vectors, wherein a sequence encoding a polypeptide of interest is placed under control of appropriate transcriptional and translational control elements to permit production or synthesis of said polypeptide. Therefore, said polynucleotide is comprised in an expression cassette. More particularly, the vector comprises a replication origin, a promoter operatively linked to said encoding polynucleotide, a ribosome binding site, a RNA-splicing site (when genomic DNA is used), a polyadenylation site and a transcription termination site. It also can comprise an enhancer or silencer elements. Selection of the promoter will depend upon the cell in which the polypeptide is expressed. Suitable promoters include tissue specific and/or inducible promoters. Examples of inducible promoters are: eukaryotic metallothionine promoter which is induced by increased levels of heavy metals, prokaryotic lacZ promoter which is induced in response to isopropyl-β-D-thiogalacto-pyranoside (IPTG) and eukaryotic heat shock promoter which is induced by increased temperature. Examples of tissue specific promoters are skeletal muscle creatine kinase, prostate-specific antigen (PSA), α-antitrypsin protease, human surfactant (SP) A and B proteins, β-casein and acidic whey protein genes.
Inducible promoters may be induced by pathogens or stress, more preferably by stress like cold, heat, UV light, or high ionic concentrations (reviewed in Potenza C et al. 2004, In vitro Cell Dev Biol 40:1-22). Inducible promoter may be induced by chemicals (reviewed in (Moore, Samalova et al. 2006); (Padidam 2003); (Wang, Zhou et al. 2003); (Zuo and Chua 2000).
Delivery vectors and vectors can be associated or combined with any cellular permeabilization techniques such as sonoporation or electroporation or derivatives of these techniques.
By cell or cells is intended any prokaryotic or eukaryotic living cells, cell lines derived from these organisms for in vitro cultures, primary cells from animal or plant origin.
By “primary cell” or “primary cells” are intended cells taken directly from living tissue (i.e. biopsy material) and established for growth in vitro, that have undergone very few population doublings and are therefore more representative of the main functional components and characteristics of tissues from which they are derived from, in comparison to continuous tumorigenic or artificially immortalized cell lines. These cells thus represent a more valuable model to the in vivo state they refer to.
In the frame of the present invention, “eukaryotic cells” refer to a fungal, plant or animal cell or a cell line derived from the organisms listed below and established for in vitro culture. More preferably, the fungus is of the genus Aspergillus, Penicillium, Acremonium, Trichoderma, Chrysoporium, Mortierella, Kluyveromyces or Pichia; More preferably, the fungus is of the species Aspergillus niger, Aspergillus nidulans, Aspergillus oryzae, Aspergillus terreus, Penicillium chrysogenum, Penicillium citrinum, Acremonium Chrysogenum, Trichoderma reesei, Mortierella alpine, Chrysosporium lucknowense, Kluyveromyces lactis, Pichia pastoris or Pichia ciferrii. 
More preferably the plant is of the genus Arabidospis, Nicotiana, Solanum, Iactuca, Brassica, Oryza, Asparagus, Pisum, Medicago, Zea, Hordeum, Secale, Triticum, Capsicum, Cucumis, Cucurbita, Citrullis, Citrus, Sorghum; More preferably, the plant is of the species Arabidospis thaliana, Nicotiana tabaccum, Solanum lycopersicum, Solanum tuberosum, Solanum melongena, Solanum esculentum, Lactuca saliva, Brassica napus, Brassica oleracea, Brassica rapa, Oryza glaberrima, Oryza sativa, Asparagus officinalis, Pisum sativum, Medicago sativa, Zea mays, Hordeum vulgare, Secale cereal, Triticum aestivum, Triticum durum, Capsicum sativus, Cucurbita pepo, Citrullus lanatus, Cucumis melo, Citrus aurantifolia, Citrus maxima, Citrus medica, Citrus reticulata. 
More preferably the animal cell is of the genus Homo, Rattus, Mus, Sus, Bos, Danio, Canis, Felis, Equus, Salmo, Oncorhynchus, Gallus, Meleagris, Drosophila, Caenorhabditis; more preferably, the animal cell is of the species Homo sapiens, Rattus norvegicus, Mus musculus, Sus scrofa, Bos taurus, Danio rerio, Canis lupus, Felis catus, Equus caballus, Salmo salar, Oncorhynchus mykiss, Gallus gallus, Meleagris gallopavo, Drosophila melanogaster, Caenorhabditis elegans. 
In the present invention, the cell can be a plant cell, a mammalian cell, a fish cell, an insect cell or cell lines derived from these organisms for in vitro cultures or primary cells taken directly from living tissue and established for in vitro culture. As non limiting examples cell lines can be selected from the group consisting of CHO-K1 cells; HEK293 cells; Caco2 cells; U2-OS cells; NIH 3T3 cells; NSO cells; SP2 cells; CHO-S cells; DG44 cells; K-562 cells, U-937 cells; MRC5 cells; IMR90 cells; Jurkat cells; HepG2 cells; HeLa cells; HT-1080 cells; HCT-116 cells; Hu-h7 cells; Huvec cells; Molt 4 cells.
All these cell lines can be modified by the method of the present invention to provide cell line models to produce, express, quantify, detect, study a gene or a protein of interest; these models can also be used to screen biologically active molecules of interest in research and production and various fields such as chemical, biofuels, therapeutics and agronomy as non-limiting examples.

    
    
        by “mutation” is intended the substitution, deletion, insertion of one or more nucleotides/amino acids in a polynucleotide (cDNA, gene) or a polypeptide sequence. Said mutation can affect the coding sequence of a gene or its regulatory sequence. It may also affect the structure of the genomic sequence or the structure/stability of the encoded mRNA.
        In the frame of the present invention, the expression “cleavage-induced mutagenesis”, preferably Double-Strand Break (DSB)-induced mutagenesis refers to a mutagenesis event consecutive to an NHEJ event following an endonuclease-induced cleavage, leading to insertion/deletion at the cleavage site of an endonuclease.
        By “gene” is meant the basic unit of heredity, consisting of a segment of DNA arranged in a linear manner along a chromosome, which codes for a specific protein or segment of protein. A gene typically includes a promoter, a 5′ untranslated region, one or more coding sequences (exons), optionally introns, a 3′ untranslated region. The gene may further comprise a terminator, enhancers and/or silencers.
        As used herein, the term “locus” is the specific physical location of a nucleic acid sequence (e.g. of a gene) on a chromosome. The term “locus” usually refers to the specific physical location of a protein or chimeric protein's nucleic acid target sequence on a chromosome. Such a locus can comprise a target sequence that is recognized and/or cleaved by a protein or a chimeric protein according to the invention. It is understood that the locus of interest of the present invention can not only qualify a nucleic acid sequence that exists in the main body of genetic material (i.e. in a chromosome) of a cell but also a portion of genetic material that can exist independently to said main body of genetic material such as plasmids, episomes, virus, transposons or in organelles such as mitochondria or chloroplasts as non-limiting examples.
        By “fusion protein” is intended the result of a well-known process in the art consisting in the joining of two or more genes which originally encode for separate proteins or part of them, the translation of said “fusion gene” resulting in a single polypeptide with functional properties derived from each of the original proteins.
        By “chimeric protein” according to the present invention is meant any fusion protein comprising at least one RVD to bind a nucleic acid sequence and one additional protein domain to process a nucleic acid target sequence within or adjacent to said bound nucleic acid sequence.
        By “additional protein domain” or “protein domain” is meant the nucleic acid target sequence processing part of said chimeric protein according to the present invention. Said protein domain can provide any catalytical activity as classified and named according to the reaction they catalyze [Enzyme Commission number (EC number) at http://www.chem.qmul.ac.uk/iubmb/enzyme/)]. Said protein domain can be a catalytically active entity by itself. Said protein domain can be a protein subdomain that needs to interact with another protein subdomain to form a dimeric protein domain active entity.
        By a “TALE-nuclease” (TALEN) is intended a fusion protein consisting of a DNA-binding domain derived from a Transcription Activator Like Effector (TALE) and one nuclease catalytic domain to cleave a nucleic acid target sequence. Said TALE-nuclease is a subclass of chimeric protein according to the present invention.
        by “variant(s)”, it is intended a RVD variant, a chimeric protein variant, a DNA binding variant, a TALE-nuclease variant, a polypeptide variant obtained by replacement of at least one residue in the amino acid sequence of the parent molecule.
        by “functional mutant” is intended a catalytically active mutant of a protein or a protein domain; such mutant can have the same activity compared to its parent protein or protein domain or additional properties. This definition applies to chimeric proteins or protein domains that constitute chimeric proteins according to the present invention. Are also encompassed in the scope of this definition “derivatives” of these proteins or protein domains that comprise the entirety or part of these proteins or protein domains fused to other proteic or chemical parts such as tags, antibodies, polyethylene glycol as non-limiting examples.
        “identity” refers to sequence identity between two nucleic acid molecules or polypeptides. Identity can be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same base, then the molecules are identical at that position. A degree of similarity or identity between nucleic acid or amino acid sequences is a function of the number of identical or matching nucleotides at positions shared by the nucleic acid sequences. Various alignment algorithms and/or programs may be used to calculate the identity between two sequences, including FASTA, or BLAST which are available as a part of the GCG sequence analysis package (University of Wisconsin, Madison, Wis.), and can be used with, e.g., default setting.
    
    


The above written description of the invention provides a manner and process of making and using it such that any person skilled in this art is enabled to make and use the same, this enablement being provided in particular for the subject matter of the appended claims, which make up a part of the original description.
As used above, the phrases “selected from the group consisting of,” “chosen from,” and the like include mixtures of the specified materials.
Where a numerical limit or range is stated herein, the endpoints are included. Also, all values and subranges within a numerical limit or range are specifically included as if explicitly written out.
The above description is presented to enable a person skilled in the art to make and use the invention, and is provided in the context of a particular application and its requirements. Various modifications to the preferred embodiments will be readily apparent to those skilled in the art, and the generic principles defined herein may be applied to other embodiments and applications without departing from the spirit and scope of the invention. Thus, this invention is not intended to be limited to the embodiments shown, but is to be accorded the widest scope consistent with the principles and features disclosed herein.
Having generally described this invention, a further understanding can be obtained by reference to certain specific examples, which are provided herein for purposes of illustration only, and are not intended to be limiting unless otherwise specified.
EXAMPLES
A first characterization of the activity, in yeast, of libraries having position 12 and/or 13 randomized (based on a HD scaffold, SEQ ID NO: 19) was performed. The randomization was performed on the RVD in position 1 and/or on the RVDs in position 1 and 2 according to the target.
Libraries on Position 12 and 13
Eight libraries (lib1 to 8) which contain only a subset of the possible 20 natural amino acids and one library (lib9) containing the 20 possible amino acids were first used. The randomization of positions 12 and 13 was performed using degenerated oligonucleotides (Table 1; SEQ ID NO: 26-39) and conventional Overlap Extension (OE) PCR techniques using a HD mono-RVD in a pAPG10 plasmid (SEQ ID NO: 40) as template.







TABLE 1







List of oligonucleotides (5′→3′) used to introduce diversity


in positions 12 and 13 in libraries of a HD bloc.












Oligo-

SEQ
Diversity













nucleo-

ID
Mono-
Di-


Library
tides
Sequences 5′->3′
NO:
RVD
RVD






A1
cccagtcacgacgttgtaaaac
26




 


Lib 1
B1
gtctccagcgcctgcttgccgcccHNSaYgctggcgatggccacctgctc
27
48
2304


 


Lib 2
B2
gtctccagcgcctgcttgccgccaBNSaYgctggcgatggccacctgctc
28
48
2304


 


Lib 3
B3
gtctccagcgcctgcttgccgcccHNaSYgctggcgatggccacctgctc
29
48
2304


 


Lib 4
B4
gtctccagcgcctgcttgccgccHBNSaYgctggcgatggccacctgctc
30
144
20736


 


Lib 5
B5
gtctccagcgcctgcttgccgccGWDMHagctggcgatggccacctgctc
31
36
1296


 


Lib 6
B6
gtctccagcgcctgcttgccgccMHaMHagctggcgatggccacctgctc
32
36
1296


 


Lib 7
B7
gtctccagcgcctgcttgccgccaSYcHNgctggcgatggccacctgctc
33
48
2304


 


Lib 8
B8
gtctccagcgcctgcttgccgccMTYcHNgctggcgatggccacctgctc
34
48
2304


 



C1
cacaggaaacagctatgaccatg
35




 



D1
ggcaagcaggcgctggagacgg
36




 


Lib 9
B9
gtctccagcgcctgcttgccgccMNNMNNgctggcgatggccacctgctc
37
1024



 



A2
cccagtcacgacgttgtaaaac
38




 



C2
cccggtaccgcatctcgagg
39









All DNA fragments used in the different steps were purified by gel extraction. In brief, for the smaller libraries (lib1-8) the 8 DNA fragment containing the randomized 6 base pairs are generated using oligonucleotides A1 (SEQ ID NO: 26) combined with B1-138 (SEQ ID NO: 27 to 34) and the complementary fragment was generated using oligonucleotides C1 (SEQ ID NO: 35) combined with D1 (SEQ ID NO: 36). The assembly PCRs were performed using oligonucleotides A1 and C1. To prepare the starting biotinylated RVD block library used for the array synthesis, the assembly PCR is amplified by PCR using primers A2 (SEQ ID NO: 38) and C2 (SEQ ID NO: 39). The PCR product is purified and digested with SfaNI. To prepare the RVD block library to be used in position 2, the assembly PCR is purified and digested with BbVI. The use of type IIS restriction enzyme allows creation of compatible overhang between blocks. For the fully randomized library, mono-RVDs were prepared as described for smaller libraries except using oligonucleotide A2 (SEQ ID NO: 38) with B9 (SEQ ID NO: 37) and C2 (SEQ ID NO: 39) instead of C1 (SEQ ID NO: 35) for the first PCR and the subsequent assembly PCR.
The final RVD arrays libraries containing 1 or 2 randomized blocks (SEQ ID NO: 41 to 58) were synthesized using a solid support method composed of consecutive restriction/ligation/washing steps as shown in FIG. 1. In brief the first library block was immobilized on a solid support through biotin/streptavidin interaction, the second library block is ligated to the first and after SfaNI digestion, the remaining of the array (i.e the RVD array out of RVD from library, SEQ ID NO: 59) pre-synthesized by the same method was ligated to the libraries. Due to the choice of the synthesis conditions, it is expected to recover up to 50% of mono-RVD libraries, the fraction of array not having a library is expected to be neglectable. The RVD arrays libraries were first cloned in a shuttle pAPG10 plasmid. The plasmid was transformed in E. coli, colonies representing between 5 and 50% of the total library diversity were scrapped from the petri dishes, and DNA recovered by standard miniprep techniques. The insert of interest is recovered by restriction (BbvI and SfaNI) followed gel extraction and cloning into a yeast expression plasmids.
Cloning of the RVD Array Collection in the TAL Backbone
The amino acid sequences of the N-terminal, C-terminal domains and RVDS were based on the AvrBs3 TAL (ref: GenBank: X16130.1, SEQ ID NO: 78). The TAL backbone used in these experiment (pCLS9944, SEQ ID NO: 60) was derived from the previously described pCLS7183 (SEQ ID NO: 61). This backbone, pCLS9944, contains an additional N-terminal NLS sequence followed by an HA tag compared to the original pCLS7183. The C-terminal and the N-terminal domains are separated by two BsmBI restriction sites. The RVD arrays libraries (SEQ ID NO: 41 to 58) were subcloned in the pCLS9944 using type IIs restriction enzymes BsmBI for the receiving plasmid and BbvI and SfaNI for the inserted RVD sequence, leading to the nine libraries. Colonies were scrapped and DNA recovered by standard miniprep techniques.
TALE-Nuclease Activities in Yeast
All the libraries (558 clones after yeast transformation) were screened on a target set containing the 16 possible bases in position 1/2, allowing using the same target set for libraries having 1 or 2 RVDs randomized. All the yeast target reporter plasmids containing the TALE-Nuclease DNA target collection sequences were constructed as previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006). The collections of TALE-Nuclease were tested at 37° C. and 30° C. in our yeast SSA assay previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) as pseudo-palindromic sequences (two identical recognition sequences are placed facing each other on both DNA strands) on their target collections (SEQ ID NO: 62 to 77, Table 2).







TABLE 2







Target collections for libraries screening.











SEQ


Name
Sequence
ID NO:












AAG_RAGT2L10
TAAGCACTTATatgtgtgtaacaggt
62



ATAAGTGCTTA



 


ACG_RAGT2L10
TACGCACTTATatgtgtgtaacaggt
63



ATAAGTGCGTA



 


AGG_RAGT2L10
TAGGCACTTATatgtgtgtaacaggt
64



ATAAGTGCCTA



 


ATG_RAGT2L10
TATGCACTTATatgtgtgtaacaggt
65



ATAAGTGCATA



 


CAG_RAGT2L10
TCAGCACTTATatgtgtgtaacaggt
66



ATAAGTGCTGA



 


CCG_RAGT2L10
TCCGCACTTATatgtgtgtaacaggt
67



ATAAGTGCGGA



 


CGG_RAGT2L10
TCGGCACTTATatgtgtgtaacaggt
68



ATAAGTGCCGA



 


CTG_RAGT2L10
TCTGCACTTATatgtgtgtaacaggt
69



ATAAGTGCAGA



 


GAG_RAGT2L10
TGAGCACTTATatgtgtgtaacaggt
70



ATAAGTGCTCA



 


GCG_RAGT2L10
TGCGCACTTATatgtgtgtaacaggt
71



ATAAGTGCGCA



 


GGG_RAGT2L10
TGGGCACTTATatgtgtgtaacaggt
72



ATAAGTGCCCA



 


GTG_RAGT2L10
TGTGCACTTATatgtgtgtaacaggt
73



ATAAGTGCACA



 


TAG_RAGT2L10
TTAGCACTTATatgtgtgtaacaggt
74



ATAAGTGCTAA



 


TCG_RAGT2L10
TTCGCACTTATatgtgtgtaacaggt
75



ATAAGTGCGAA



 


TGG_RAGT2L10
TTGGCACTTATatgtgtgtaacaggt
76



ATAAGTGCCAA



 


TTG_RAGT2L10
TTTGCACTTATatgtgtgtaacaggt
77



ATAAGTGCAAA









TALE-Nuclease cleavage activity levels of individual clones of the library on the complete collection of targets in yeast were recorded. Plasmid DNA of clones having activity on at least one target was recovered using standard yeast biology techniques, transformed in E. coli and plasmid DNA from individual colonies were recovered by standard molecular biology techniques. The plasmid DNA were sequenced and retransformed in yeast for a secondary screen. Table 3 represents the mean activity (screen 1 and 2) of three clones in which RVD 1 was randomized (SEQ ID NO: 23 to 25) recovered from a subset of the libraries.







TABLE 3







Mean activities of three clones with one RVD randomized on a


serie of targets (SEQ ID NO: 62-77) in our yeast SSA assay previously


described (International PCT Applications WO 2004/067736 and in


(Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould,


Chames et al. 2006; Smith, Grizot et al. 2006) at 30° C. − indicates


no detectable activity, + indicates low activity, ++ medium


activity and +++ high activity.









Targeted base












A
C
G
T

















Varia-
Classical
HD (SEQ ID NO: 19)
++
++
+
+++


ble

NN (SEQ ID NO: 20)
+++
+/−
+++
−


di-

NG (SEQ ID NO: 21)
++
+++
+/−
−


residue

NI (SEQ ID NO: 22)
+++
+/−
+
−



New
TL (SEQ ID NO: 23)
+++
−
−
−




VT (SEQ ID NO: 24)
+++
+/−
+++
−




SW (SEQ ID NO: 25)
+/−
−
−
−









Example 2
To design new RVD/target pairs (in the context of a TALE-nuclease) an extensive characterization of the activity in yeast of libraries having position 12 and/or 13 randomized was performed. The randomization was performed in NNK libraries on positions 12 and 13 of a repeat unit inserted at position 1 to 4 of the array of 9.5 repeat units.
The randomization of positions 12 and 13 was performed using degenerated oligonucleotides (Table 4, SEQ ID NO: 79-84) and conventional Overlap Extension (OE) PCR techniques using a NG mono-repeat unit (SEQ ID NO: 85) in a pAPG10 plasmid (SEQ ID NO: 86) as template. All DNA fragments used in the different steps were purified by appropriate techniques. In brief, the DNA fragment containing the randomized 6 base pairs are generated using oligonucleotide E1 (SEQ ID NO: 79) combined with E2 (SEQ ID NO: 80) leading to FRAG1 and the complementary fragment was generated using oligonucleotides F1 (SEQ ID NO: 81) combined with F2 (SEQ ID NO: 82) leading to FRAG2. The assembly PCR of FRAG1 and FRAG2 was performed using oligonucleotides G1 (SEQ ID NO: 83) and G2 (SEQ ID NO: 84) to allow biotinylation of the fragment. The PCR product are further purified and digested with SfaNI.







TABLE 4







List of oligonucleotides (5′→3′) used to


introduce diversity in position 12 and


13 of a NG bloc.








Oligo-










nucleo-

SEQ


tide

ID


Names
Sequences
NO:





Oligo E1
cccagtcacgacgttgtaaaac
79


 


Oligo E2
gtctccagcgcctgcttgccgccMNNMNNgctggc
80



gatggccaccacctgctc



 


Oligo F1
ggcaagcaggcgctggagacgg
81


 


Oligo F2
cacaggaaacagctatgaccatg
82


 


Oligo G1
Biotin-cccagtcacgacgttgtaaaac
83


 


Oligo G2
cccggtaccgcatctcgagg
84









Library a in Position 1 of the Array

For this collection in position 1 of the TALE array, the desired building block coding for TALE array A2-A10 (SEQ ID NO: 87) was pre-prepared (BbvI digested) and coupled (ligated) to the immobilized bloc (randomized in positions 12 and 13) via a solid support technology (FIG. 2). The final product was recovered using enzymatic restriction (SfaNI and BbvI digestions) and cloned in a yeast pCLS9944 expression plasmid (SEQ ID NO: 60). After transformation in E. coli, 1200 colonies were individually picked, grown overnight and plasmid DNA extracted using standard procedures.
Libraries B, C and D in Position 2, 3 and 4 of the Array
For these libraries in position 2, 3 and 4 of the TALE array, the desired building blocks coding for RVD array B03-B10 (SEQ ID NO: 88) for library B, C04-C10 (SEQ ID NO: 89) for library C and D05-D10 (SEQ ID NO: 90) for library D were pre-prepared and coupled to the randomized bloc via a solid support technology and steps of enzymatic restrictions and digestions. The coupled intermediate products were then subcloned in the shuttle pAGG10 plasmid. Colonies (at least 4 time the diversity of the libraries) were scraped from the agarose plates, plasmid DNA were extracted using standard techniques and the intermediate array constructs containing the randomized bloc in position 1 were recovered using enzymatic restriction (BbvI and SfiI). These intermediate array constructs containing the randomized bloc in position 1 were coupled (ligated) to immobilized blocs coding for, B01 (SEQ ID NO: 91) for library B, C01-C002 (SEQ ID NO: 92) for library C and D01-D03 (SEQ ID NO: 93) for library D, via a solid support technology (FIG. 2). The final products were recovered using enzymatic restriction (SfaNI and BbvI digestions) and cloned in a yeast expression plasmid pCLS9944 (SEQ ID NO: 60). After transformation in E. coli, 1200 colonies were individually picked, grown overnight and plasmid DNA extracted using standard procedures.
TALE-Nuclease Library Activities in Yeast
DNA plasmids coding for all members of the libraries, were individually transformed in yeast cells, leading to 1144, 1149, 1148 and 1150 transformants for the library A, B, C and D respectively.
All the yeast target reporter plasmids containing the TALE-Nuclease DNA target collection sequences were constructed as previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006). The libraries of TALE-Nuclease were tested at 37° C. and 30° C. in our yeast SSA assay previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) as pseudo-palindromic sequences (two identical recognition sequences are placed facing each other on both DNA strands) on their respective targets (containing A, C, G or T at the position of the library bloc, Table 5, SEQ ID NO: 94 to SEQ ID NO: 109).









TABLE 5







SEQ


Target

ID


Names
Target Sequences
NO:

















Target position
TAGTTACTTATatgtgtgtaacaggt
94


1 A
ATAAGTAACTA



 


target position
TCGTTACTTATatgtgtgtaacaggt
95


1 C
ATAAGTAACGA



 


target position
TGGTTACTTATatgtgtgtaacaggt
96


1 G
ATAAGTAACCA



 


target position
TTGTTACTTATatgtgtgtaacaggt
97


1 T
ATAAGTAACAA



 


target position
TTAGCACTTATatgtgtgtaacaggt
98


2 A
ATAAGTGCTAA



 


target position
TTCGCACTTATatgtgtgtaacaggt
99


2 C
ATAAGTGCGAA



 


target position
TTGGCACTTATatgtgtgtaacaggt
100


2 G
ATAAGTGCCAA



 


target position
TTTGCACTTATatgtgtgtaacaggt 
101


2 T
ATAAGTGCAAA



 


target position
TGGATACTTATatgtgtgtaacaggt 
102


3 A
ATAAGTATCCA



 


target position
TGGCTACTTATatgtgtgtaacaggt 
103


3 C
ATAAGTAGCCA



 


target position
TGGGTACTTATatgtgtgtaacaggt 
104


3 G
ATAAGTACCCA



 


target position
TGGTTACTTATatgtgtgtaacaggt 
105


3 T
ATAAGTAACCA



 


target position
TGGTAACTTATatgtgtgtaacaggt 
106


4 A
ATAAGTTACCA



 


target position
TGGTCACTTATatgtgtgtaacaggt 
107


4 C
ATAAGTGACCA



 


target position
TGGTGACTTATatgtgtgtaacaggt 
108


4 G
ATAAGTCACCA



 


target position
TGGTTACTTATatgtgtgtaacaggt
109


4 T
ATAAGTAACCA





List of pseudo-palindromic sequences targets (two identical recognition sequences are placed facing each other on both DNA strands) in our yeast SSA assay previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) at 30° C., used for activity screens in yeast of libraries A, B, C and D.






TALE-Nuclease cleavage activities were recorded for all members of the libraries and are summarized in FIGS. 3, 4, 5 and 6 for the libraries A, B, C and D respectively. DNA of 101, 105, 136 and 128 (for the library A, B, C and D respectively) clones was sequenced.
Insertion of Non-Natural RVDs in 15.5 Repeats Arrays and Activities in Yeast
DNA coding for arrays containing non-natural RVDs in position 7 and 11 of the arrays was synthesized and subcloned in a pAPG10 plasmid (GeneCust) (SEQ ID NO: 86) leading to array pCLS19101 (NM in position 7 and LP in position 11) (SEQ ID NO: 110) and array pCLS19102 (SD in position 7 and VG in position 11) (SEQ ID NO: 111). The repeats containing arrays were then subcloned in a yeast expression plasmid pCLS9944 (SEQ ID NO: 60) using BsmBI restriction enzyme and standard molecular biology procedures leading to respectively half-TALE-Nuclease pCLS20349 (SEQ ID NO: 112) and pCLS20350 (SEQ ID NO: 113). The pendant of these two half-TALE-Nuclease containing only the canonical 4 RVDs (NI, HD, NG and NN) as well as the second half-TALE-Nuclease allowing the formation of an heterodimeric TALE-Nuclease were synthesized using solid support methods and subcloned in a yeast expression plasmid pCLS9944 (SEQ ID NO: 60) leading to respectively pCLS20735 (SEQ ID NO: 114) and pCLS20736 (SEQ ID NO: 115).
All the yeast target reporter plasmids were constructed as previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006). The TALE-Nucleases were tested at 37° C. in our yeast SSA assay previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) as heterodimeric sequences (two different recognition sequences are placed facing each other on both DNA strands) on 2 targets (A and B) varying at bases 7 and 11 (respective to the T0) (Table 6, SEQ ID NO: 116 to SEQ ID NO: 117).









TABLE 6





Target

SEQ


Names
Target sequences
ID NO:

















Target A
TCTGACACAACTGTGTTcactagcaacctcaa
116



ACAGACACCATGGTGCA



 


Target B
TCTGACATAACAGTGTTcactagcaacctcaa
117



ACAGACACCATGGTGCA





List of heterodimeric sequences targets A and B varying at bases 7 and 11 (two different recognition sequences are placed facing each other on both DNA strands) in our yeast SSA assay previously described (International PCT Applications WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames, Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot et al. 2006) at 37° C., used for activity screens in yeast of NM/LP and SD/VG containing half-TALE-Nuclease






TALE-Nuclease cleavage activities were recorded for all three pairs pCLS20349/pCLS20736; pCLS20350/pCLS20736 and pCLS20735/pCLS20736 (Table 7). These results confirm that the news RVDs characterized in the present invention have a higher specificity than RVDs previously described (WO2011/146121).







TABLE 7







Activities of the three TALE-Nuclease pairs on heterodimeric


sequence target A and B (two identical recognition sequences


are placed facing each other on both DNA strands) in our yeast


SSA assay previously described (International PCT Applications


WO 2004/067736 and in (Epinat, Arnould et al. 2003; Chames,


Epinat et al. 2005; Arnould, Chames et al. 2006; Smith, Grizot


et al. 2006) at 30° C. ++ indicates medium activity


and +++ high activity.










Target A
Target B















pCLS20349/pCLS20736
+++
++



pCLS20350/pCLS20736
+++
+++



pCLS20735/pCLS20736
+++
+++










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## Claims

1. A method for modifying the genetic material of a cell comprising:
(a) selecting a nucleic acid target sequence present on a chromosome of a mammalian cell;
(b) engineering a protein comprising at least:
(i) one Transcription Activator-Like Effector (TALE) domain wherein said TALE domain comprises a plurality of TALE repeat sequences comprising each one a Repeat Variable Diresidue region (RVD) which is responsible for the binding to one specific nucleotide in the nucleic acid target sequence present on a chromosome of the mammalian cell, wherein one or more RVD is selected from the group consisting of:
PI, DL, FL, GL, IL, KL, LL, YL, MM, WY, PV, SW, XF for recognizing A, wherein X represents one amino acid residue selected from the group consisting of A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, and K;
RE for recognizing C;
ER, FR, GR, LR, QR, VR for recognizing G; and
(ii) an endonuclease domain to cleave genetic material within the nucleic acid target sequence;

(c) contacting said engineered protein with said nucleic acid target sequence in the mammalian cell such that the engineered protein binds to the nucleic acid target sequence and cleaves the chromosome within the nucleic acid target sequence to create a double strand break,
wherein the double strand break is repaired by the cell through non-homologous end joining (NHEJ) resulting in a genetic modification in the chromosome.

2. A method for inducing homologous gene targeting in a mammalian cell comprising:
(a) providing a mammalian cell comprising a nucleic acid target sequence present on a chromosome;
(b) engineering a chimeric protein comprising at least:
(i) one Transcription Activator-Like Effector (TALE) domain wherein said TALE domain comprises a plurality of TALE repeat sequences comprising each one a Repeat Variable Diresidue region (RVD) which is responsible for the binding to one specific nucleotide in the nucleic acid target sequence present on a chromosome of the mammalian cell, wherein one or more RVD is selected from the group consisting of:
PI, DL, FL, GL, IL, KL, LL, YL, MM, WY, PV, SW, XF for recognizing A, wherein X represents one amino acid residue selected from the group consisting of A, G, V, L, I, M, S, T, C, P, D, E, F, Y, W, Q, N, and K;
RE for recognizing C;
ER, FR, GR, LR, QR, VR for recognizing G; and
(ii) an endonuclease domain to cleave genetic material within the nucleic acid target sequence; and

(c) introducing said chimeric protein into said mammalian cell such that the engineered protein binds to the nucleic acid target sequence and cleaves the chromosome within the nucleic acid target sequence to create a double strand break,
(d) introducing into the cell an exogenous nucleic acid comprising a sequence homologous to at least a portion of the nucleic acid target sequence,
wherein homologous recombination occurs between said exogenous nucleic acid and the nucleic acid target sequence processes genetic material within or adjacent to the specific nucleic acid target sequence.

3. A method for generating an animal comprising:
(a) providing a cell comprising a nucleic acid target sequence into which it is desired to introduce a genetic modification;
(b) modifying the genetic material of a cell according to the method of claim 1;
(c) generating an animal from the cell or progeny thereof, in which a genetic modification has occurred.

4. The method according to claim 2, wherein the cell is a human cell.

5. The method of claim 2, wherein one or more RVD is selected from the group consisting of:
PI, DL, FL, GL, IL, KL, LL, YL, MM, WY, PV, SW, XF for recognizing A.

6. The method of claim 2, wherein one or more RVD is selected from the group consisting of:
RE for recognizing C.

7. The method of claim 2, wherein one or more RVD is selected from the group consisting of:
ER, FR, GR, LR, QR, VR for recognizing G.

8. The method of claim 1, wherein one or more RVD is selected from the group consisting of:
PI, DL FL, GL, IL, KL, LL, YL, MM, WY, PV, SW, XF for recognizing A.

9. The method of claim 1, wherein one or more RVD is selected from the group consisting of:
RE for recognizing C.

10. The method of claim 1, wherein one or more RVD is selected from the group consisting of:
ER, FR, GR, LR, QR, VR for recognizing G.

11. The method of claim 1, wherein the genetic modification is a deletion.

12. The method of claim 1, wherein the genetic modification is an insertion.

13. The method of claim 1, wherein the genetic modification is a combination of both a deletion and an insertion.