Nucleotide-specific recognition sequences for designer TAL effectors
View Patent ↗The invention relates to methods of altering expression of a genomic locus of interest or specifically targeting a genomic locus of interest in an animal cell, which may involve contacting the genomic locus with a non-naturally occurring or engineered composition that includes a deoxyribonucleic acid (DNA) binding polypeptide having a N-terminal capping region, a DNA binding domain comprising at least five or more Transcription activator-like effector (TALE) monomers and at least one or more half-monomers specifically ordered to target the genomic locus of interest, and a C-terminal capping region, wherein the polypeptide includes at least one or more effector domains, and wherein the polypeptide is encoded by and translated from a codon optimized nucleic acid molecule so that the polypeptide preferentially binds to the DNA of the genomic locus.
1. A method of selectively targeting a genomic locus of interest comprising a coding or regulatory sequence susceptible to being affected by an effector domain in an animal cell, comprising contacting the genomic locus with a non-naturally occurring or engineered composition comprising a DNA binding polypeptide comprising:
(a) a N-terminal capping region
(b) a DNA binding domain comprising at least 5 to 40 Transcription activator-like effector (TALE) monomers and at least one or more half-monomers specifically ordered to target the genomic locus of interest, and
(c) a C-terminal capping region
wherein (a), (b) and (c) are arranged in a predetermined N-terminus to C-terminus orientation,
wherein the polypeptide includes at least one or more effector domains,
wherein the polypeptide is encoded by and translated from a codon optimized nucleic acid molecule so that the polypeptide preferentially binds to DNA of the genomic locus,
wherein the genomic locus comprises a target DNA sequence 5′-T 0 N 1 N 2 . . . N z N z+1 -3′, where T 0 and N=A, G, T or C,
wherein the target DNA sequence binds to the DNA binding domain, and the DNA binding domain comprises (X 1-11 -X 12 X 13 -X 14-33 or 34 or 35 ) z ,
wherein X 1-11 is a chain of 11 contiguous amino acids,
wherein X 12 X 13 is a repeat variable diresidue (RVD),
wherein X 14-33 or 34 or 35 is a chain of 21, 22 or 23 contiguous amino acids,
wherein z is at least 5 to 40,
wherein [LTLD] (SEQ ID NO: 1) is present at X 1-4 , and
wherein at least one RVD is selected from the group consisting of (a) HH, KH, NH, NK, NQ, RH, RN, SS, KN for recognition of guanine (G); (b) KI, RI, HI, SI for recognition of adenine (A); (c) KG, RG for recognition of thymine (T); (d) RD, SD, KD, YG for recognition of cytosine (C); (e) NV, HN for recognition of A or G; and (f) HA, KA, NC, NS, RA, S* for recognition of A or T or G or C, wherein (*) means that the amino acid at X 13 is absent,
or
wherein [LTLA] (SEQ ID NO: 2) is present at X 1-4 , and
wherein at least one RVD is selected from the group consisting of (a) HH, KH, NH, NK, NQ, RH, RN, SS, SN, KN for recognition of guanine (G); (b) KI, RI, HI, SI for recognition of adenine (A); (c) KG, RG for recognition of thymine (T); (d) RD, SD, HD, KD, YG for recognition of cytosine (C); (e) NV, HN for recognition of A or G; and (f) H*, HA, KA, N*, NA, NC, NS, RA, S* for recognition of A or T or G or C, wherein (*) means that the amino acid at X 13 is absent,
or
wherein [EQHG] (SEQ ID NO: 4) is present at positions X 30-33 or X 31-34 or X 32-35 , and
wherein at least one RVD is selected from the group consisting of (a) HH, KH, NH, NK, NQ, RH, RN, SS, SN, KN for recognition of guanine (G); (b) KI, RI, HI, SI for recognition of adenine (A); (c) HG, KG, RG for recognition of thymine (T); (d) RD, SD, ND, KD, YG for recognition of cytosine (C); (e) FIN for recognition of A or G; and (f) H*, HA, KA, N*, NA, NC, RA, S* for recognition of A or T or G or C, wherein (*) means that the amino acid at X 13 is absent,
and
wherein selectively targeting the genomic locus comprises specific recognition between the target DNA sequence and the polypeptide corresponding to the genomic locus of interest in the animal cell contacted with the polypeptide and an effect on the genomic locus of interest by the effector domain, as compared to a control animal cell in which the genomic locus of interest is contacted with a control polypeptide that does not have at least one or more effector domains.
2. The method according to claim 1 , wherein the effector domain is an activator domain, a repressor domain, a DNA methyltransferase domain, a recombinase domain or a nuclease domain.
3. The method according to claim 1 , wherein
the RVD for the recognition of G is RN, NH, RH or KH; or
the RVD for the recognition of A is SI; or
the RVD for the recognition of T is KG or RG; and
the RVD for the recognition of C is SD or RD.
4. The method according to claim 1 , wherein
the N-terminal capping region or fragment thereof comprises 147 contiguous amino acids of a wild type N-terminal capping region, or
the C-terminal capping region or fragment thereof comprises 68 contiguous amino acids of a wild type C-terminal capping region, or
the N-terminal capping region or fragment thereof comprises 136 contiguous amino acids of a wild type N-terminal capping region and the C-terminal capping region or fragment thereof comprises 183 contiguous amino acids of a wild type C-terminal capping region.
5. The method according to claim 1 , wherein the sequence X 1-11 -X 12 X 13 -X 14-33 or 34 or 35 is selected from the group consisting of:
(SEQ ID NO: 356)
LTLDQVVAIAS X 12 X 13 GGKQALETVQRLLPVLCQDHG,
(SEQ ID NO: 357)
LTLDQVVAIAS X 12 X 13 GGKQALETVQRLLPVLCQAHG,
(SEQ ID NO: 358)
LTLDQVVAIAS X 12 X 13 GSKQALETVQRLLPVLCQDHG,
(SEQ ID NO: 359)
LTLDQVVAIAS X 12 X 13 GGKKALETVQRLLPVLCQDHG,
(SEQ ID NO: 360)
LTLDKVVAIAS X 12 X 13 GGKQALETVQRLLPVLCQDHG,
(SEQ ID NO: 361)
LTLDQVVAIAS X 12 X 13 GSKQALETVQRLLPVLCQAHG,
(SEQ ID NO: 362)
LTLDQVVAIAS X 12 X 13 GGKQALETVQRLLPVLCQARG,
(SEQ ID NO: 363)
LTLDQVVAIAS X 12 X 13 GGKQALETVQRLLPVLCEQHG,
(SEQ ID NO: 364)
LTLDQVVAIAS X 12 X 13 GGKQALETVQRLLPVLCQTHG,
(SEQ ID NO: 365)
LTLDQVAAIAS X 12 X 13 GGKQALETVQRLLPVLCQAHG,
(SEQ ID NO: 366)
LTLDQVVAIAS X 12 X 13 GSKQALETVQRLLPVLCQTHG,
(SEQ ID NO: 367)
LTLDQVVAIAS X 12 X 13 GGKQALETVQRLLPVLCQEHG,
and
(SEQ ID NO: 368)
LTLDQVVSIAS X 12 X 13 GGKQALETVQRLLPVLCQDHG.
6. The method according to claim 1 , wherein the sequence X 1-11 -X 12 X 13 -X 14-33 or 34 or 35 is selected from the group consisting of:
(SEQ ID NO: 369)
LTLAQVVAIAS X 12 X 13 GGKQALETVQRLLPVLCQAHG,
(SEQ ID NO: 370)
LTLAQVVAIAS X 12 X 13 GGKQALETVQRLLPVLCQDHG,
(SEQ ID NO: 371)
LTLAQVVAIAN X 12 X 13 GGKQALETVQRLLPVLCQAHG,
(SEQ ID NO: 372)
LTLAQVVAIAN X 12 X 13 GGKQALETVQRLLPVLCQDHG,
and
(SEQ ID NO: 373)
LTLAQVVAIAS X 12 X 13 GGKQALETVQRLLPVLCQTHG.
7. The method according to claim 1 , wherein the sequence X 1-11 -X 12 X 13 -X 14-33 or 34 or 35 is selected from the group consisting of:
(SEQ ID NO: 376)
LTPDQVVAIAS X 12 X 13 GGKQALETVQRLLPVLCEQHG,
(SEQ ID NO: 377)
LTPAQVVAIAS X 12 X 13 GGKQALETVQQLLPVLCEQHG,
(SEQ ID NO: 378)
LTPAQVVAIAS X 12 X 13 GGKQALETVQRLLPVLCEQHG,
(SEQ ID NO: 379)
LTPDQVVAIAS X 12 X 13 GGRPALETVQRLLPVLCEQHG,
(SEQ ID NO: 380)
LTPAQVVAIAS X 12 X 13 GGKQALKTVQQLLPVLCEQHG,
(SEQ ID NO: 381)
LTPDQVVAIAS X 12 X 13 GGKQALERVQRLLPVLCEQHG,
(SEQ ID NO: 382)
LTRAQVVAIAS X 12 X 13 GGKQALETVQRLLPVLCEQHG,
(SEQ ID NO: 383)
LTLDQVVAIAS X 12 X 13 GGKQALETVQRLLPVLCEQHG,
(SEQ ID NO: 384)
LTPAQVVTIAS X 12 X 13 GGKQALETVQRLLPVLCEQHG,
(SEQ ID NO: 385)
LTPQQVVAIAS X 12 X 13 GGKQALETVQRLLPVLCEQHG,
(SEQ ID NO: 386)
LTPAQVVAIAS X 12 X 13 GGKPALETVQRLLPVLCEQHG,
(SEQ ID NO: 387)
LTPDQVVAIAS X 12 X 13 GGRQALETVQRLLPVLCEQHG,
and
(SEQ ID NO: 388)
LTPDQVVAIAS X 12 X 13 GGKPALETVQRLLPVLCEQHG.
8. A method of selectively targeting a genomic locus of interest comprising a coding or regulatory sequence susceptible to being affected by an effector domain in an animal cell, comprising contacting the genomic locus with a non-naturally occurring or engineered composition comprising a DNA binding polypeptide comprising:
(a) a N-terminal capping region
(b) a DNA binding domain comprising at least 5 to 40 Transcription activator-like effector (TALE) monomers and at least one or more half-monomers specifically ordered to target the genomic locus of interest, and
(c) a C-terminal capping region
wherein (a), (b) and (c) are arranged in a predetermined N-terminus to C-terminus orientation,
wherein the polypeptide includes at least one or more effector domains,
wherein the polypeptide is encoded by and translated from a codon optimized nucleic acid molecule so that the polypeptide preferentially binds to DNA of the genomic locus,
wherein the genomic locus comprises a target DNA sequence 5′-T 0 N 1 N 2 . . . N z N z+1 -3′, where T 0 and N=A, G, T or C,
wherein the target DNA sequence binds to the DNA binding domain, and the DNA binding domain comprises (X 1-11 -X 12 X 13 -X 14-33 or 34 or 35 ) z ,
wherein X 1 is a chain of 11 contiguous amino acids,
wherein X 12 X 13 is a repeat variable diresidue (RVD),
wherein X 14-33 or 34 or 35 is a chain of 21, 22 or 23 contiguous amino acids,
wherein z is at least 5 to 40,
wherein [LTQV] (SEQ ID NO: 3) is present at X 14 , and
wherein at least one RVD is selected from the group consisting of (a) HH, KH, NH, NK, NQ, RH, RN, SS, NN, SN, KN for recognition of guanine (G); (b) KI, RI, HI, SI for recognition of adenine (A); (c) NG, HG, KG, RG for recognition of thymine (T); (d) RD, SD, HD, ND, KD, YG for recognition of cytosine (C); (e) NV, HN for recognition of A or G; and (f) H*, HA, KA, N*, NA, NC, NS, RA, S* for recognition of A or T or G or C, wherein (*) means that the amino acid at X 13 is absent,
or
wherein [RDHG] (SEQ ID NO: 5) is present at positions X 30-33 or X 31-34 or X 32-35 , and
wherein at least one RVD is selected from the group consisting of (a) HH, KH, NH, NK, NQ, RH, RN, SS, NN, SN, KN for recognition of guanine (G); (b) KI, RI, HI, SI for recognition of adenine (A); (c) NG, HG, KG, RG for recognition of thymine (T); (d) RD, SD, HD, ND, KD, YG for recognition of cytosine (C); (e) NV, HN for recognition of A or G; and (f) H*, HA, KA, N*, NA, NC, RA, S* for recognition of A or T or G or C, wherein (*) means that the amino acid at X 13 is absent,
and
wherein selectively targeting the genomic locus comprises specific recognition between the target DNA sequence and the polypeptide corresponding to the genomic locus of interest in the animal cell contacted with the polypeptide and an effect on the genomic locus of interest by the effector domain, as compared to a control animal cell in which the genomic locus of interest is contacted with a control polypeptide that does not have at least one or more effector domains.
9. The method according to claim 8 , wherein the effector domain is an activator domain, a repressor domain, a DNA methyltransferase domain, a recombinase domain or a nuclease domain.
10. The method according to claim 8 , wherein
the RVD for the recognition of G is RN, NH, RH or KH; or
the RVD for the recognition of A is SI; or
the RVD for the recognition of T is KG or RG; and
the RVD for the recognition of C is SD or RD.
11. The method according to claim 8 , wherein
the N-terminal capping region or fragment thereof comprises 147 contiguous amino acids of a wild type N-terminal capping region, or
the C-terminal capping region or fragment thereof comprises 68 contiguous amino acids of a wild type C-terminal capping region, or
the N-terminal capping region or fragment thereof comprises 136 contiguous amino acids of a wild type N-terminal capping region and the C-terminal capping region or fragment thereof comprises 183 contiguous amino acids of a wild type C-terminal capping region.
12. The method according to claim 8 , wherein the sequence X 1-11 -X 12 X 13 -X 14-33 or 34 or 35 is LTQVQVVAIAS X 12 X 13 GGKQALETVQRLLPVLCQAHG (SEQ ID NO: 374).
13. The method according to claim 8 , wherein the sequence X 1-11 -X 12 X 13 -X 14-33 or 34 or 35 is LTPDQVVAIASX 12 X 13 GGKQALETVQRLLPVLCRDHG (SEQ ID NO: 389) or LTPAQVVAIAS X 12 X 13 GGKQALETVQRLLPVLCRDHG (SEQ ID NO: 390).
14. A method of selectively targeting a genomic locus of interest comprising a coding or regulatory sequence susceptible to being affected by an effector domain in an animal cell, comprising contacting the genomic locus with a non-naturally occurring or engineered composition comprising a DNA binding polypeptide comprising:
(a) a N-terminal capping region
(b) a DNA binding domain comprising at least 5 to 40 Transcription activator-like effector (TALE) monomers and at least one or more half-monomers specifically ordered to target the genomic locus of interest, and
(c) a C-terminal capping region
wherein (a), (b) and (c) are arranged in a predetermined N-terminus to C-terminus orientation,
wherein the polypeptide includes at least one or more effector domains,
wherein the polypeptide is encoded by and translated from a codon optimized nucleic acid molecule so that the polypeptide preferentially binds to DNA of the genomic locus,
wherein the genomic locus comprises a target DNA sequence 5′-T 0 N 1 N 2 . . . N z N z+1 -3′, where T 0 and N=A, G, T or C,
wherein the target DNA sequence binds to the DNA binding domain, and the DNA binding domain comprises (X 1-11 -X 12 X 13 -X 14-33 or 34 or 35 ) z ,
wherein X 1-11 is a chain of 11 contiguous amino acids,
wherein X 12 X 13 is a repeat variable diresidue (RVD),
wherein X 14-33 or 34 or 35 is a chain of 21, 22 or 23 contiguous amino acids,
wherein z is at least 5 to 40,
wherein the sequence X 1-11 -X 12 X 13 -X 14-33 or 34 or 35 is LTLTQVVAIAS X 12 X 13 GGKQALETVQRLLPVLCQAHG (SEQ ID NO: 375),
wherein at least one RVD is selected from the group consisting of (a) HH, KH, NH, NK, NQ, RH, RN, SS, NN, SN, KN for recognition of guanine (G); (b) NI, KI, RI, HI, SI for recognition of adenine (A); (c) HG, KG, RG for recognition of thymine (T); (d) RD, SD, HD, ND, KD, YG for recognition of cytosine (C); (e) NV, HN for recognition of A or G; and (f) H*, HA, KA, N*, NA, NC, NS, RA, S* for recognition of A or T or G or C, wherein (*) means that the amino acid at X 13 is absent, and
wherein selectively targeting the genomic locus comprises specific recognition between the target DNA sequence and the polypeptide corresponding to the genomic locus of interest in the animal cell contacted with the polypeptide and an effect on the genomic locus of interest by the effector domain, as compared to a control animal cell in which the genomic locus of interest is contacted with a control polypeptide that does not have at least one or more effector domains.