Methods and compositions for targeted cleavage and recombination
First Claim
1. A method for cleaving genomic cellular chromatin in a region of interest of an isolated cell, the method comprising:
- (a) selecting first and second nucleotide sequences in the region of interest;
(b) engineering first and second zinc finger binding domains to bind to the first and second nucleotide sequences;
(c) constitutively expressing a first fusion protein in a cell, the first fusion protein comprising the first engineered zinc finger binding domain and a first FokI cleavage half-domain;
(d) constitutively expressing a second fusion protein in the cell, the second fusion protein comprising;
(i) the second zinc finger binding domain; and
(ii) a second Fold cleavage half-domain;
wherein one of the cleavage half-domains comprises an alteration in amino acid 490 of the wild-type dimerization interface of the cleavage half-domain, the first fusion protein binds to the first nucleotide sequence, the second fusion protein binds to the second nucleotide sequence located between 2 and 50 nucleotides from the first nucleotide sequence, and the cellular chromatin is cleaved in the region of interest.
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Abstract
Disclosed herein are methods and compositions for targeted cleavage of a genomic sequence, targeted alteration of a genomic sequence, and targeted recombination between a genomic region and an exogenous polynucleotide homologous to the genomic region. The compositions include fusion proteins comprising a cleavage domain (or cleavage half-domain) and an engineered zinc finger domain and polynucleotides encoding same. Methods for targeted cleavage include introduction of such fusion proteins, or polynucleotides encoding same, into a cell. Methods for targeted recombination additionally include introduction of an exogenous polynucleotide homologous to a genomic region into cells comprising the disclosed fusion proteins.
171 Citations
38 Claims
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1. A method for cleaving genomic cellular chromatin in a region of interest of an isolated cell, the method comprising:
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(a) selecting first and second nucleotide sequences in the region of interest; (b) engineering first and second zinc finger binding domains to bind to the first and second nucleotide sequences; (c) constitutively expressing a first fusion protein in a cell, the first fusion protein comprising the first engineered zinc finger binding domain and a first FokI cleavage half-domain; (d) constitutively expressing a second fusion protein in the cell, the second fusion protein comprising; (i) the second zinc finger binding domain; and (ii) a second Fold cleavage half-domain; wherein one of the cleavage half-domains comprises an alteration in amino acid 490 of the wild-type dimerization interface of the cleavage half-domain, the first fusion protein binds to the first nucleotide sequence, the second fusion protein binds to the second nucleotide sequence located between 2 and 50 nucleotides from the first nucleotide sequence, and the cellular chromatin is cleaved in the region of interest. - View Dependent Claims (2)
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3. A method for cleaving genomic cellular chromatin in a region of interest in an isolated cell, the method comprising:
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(a) selecting the region of interest; (b) engineering a first zinc finger binding domain to bind to a first nucleotide sequence in the region of interest; (c) engineering a second zinc finger binding domain to bind to a second nucleotide sequence in the region of interest, wherein the second sequence is located between 2 and 50 nucleotides from the first sequence; (d) constitutively expressing a first fusion protein in a cell, the first fusion protein comprising the first zinc finger binding domain and a first FokI cleavage half-domain; and (e) constitutively expressing a second fusion protein in the cell, the second fusion protein comprising the second zinc finger binding domain and a second FokI cleavage half domain; wherein one of the cleavage half-domains comprises an alteration in amino acid 490 of the wild-type dimerization interface of the cleavage half-domain, the first fusion protein binds to the first nucleotide sequence, and the second fusion protein binds to the second nucleotide sequence, and further wherein said binding positions the cleavage half-domains such that the cellular chromatin is cleaved in the region of interest. - View Dependent Claims (4, 5)
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6. A method for altering a first nucleotide sequence in a region of interest in cellular chromatin in an isolated cell, the method comprising:
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(a) engineering a first zinc finger binding domain to bind to a second nucleotide sequence in the region of interest, wherein the second sequence comprises at least 9 nucleotides; (b) engineering a second zinc finger binding domain to bind to a third nucleotide sequence, wherein the third sequence comprises at least 9 nucleotides and is located between 2 and 50 nucleotides from the second sequence; (c) constitutively expressing a first fusion protein in a cell, the first fusion protein comprising the first zinc finger binding domain and a first FokI cleavage half-domain; (d) constitutively expressing a second fusion protein in the cell, the second fusion protein comprising the second zinc finger binding domain and a second FokI cleavage half domain, wherein one of the cleavage half-domains comprises an alteration in amino acid 490 of the wild-type dimerization interface of the cleavage half-domain; and (e) contacting the cell with a polynucleotide comprising a fourth nucleotide sequence, wherein the fourth nucleotide sequence is homologous but non-identical with the first nucleotide sequence; wherein binding of the first fusion protein to the second sequence, and binding of the second fusion protein to the third sequence, positions the cleavage half-domains such that the cellular chromatin is cleaved in the region of interest, thereby facilitating homologous recombination between the first nucleotide sequence and the fourth nucleotide sequence, resulting in alteration of the first nucleotide sequence. - View Dependent Claims (7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28)
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29. A method for altering a first nucleotide sequence in a region of interest in cellular chromatin in an isolated cell, the method comprising:
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(a) engineering a zinc finger binding domain to bind to a second nucleotide sequence in the region of interest, wherein the second sequence comprises at least 9 nucleotides; (b) constitutively expressing a fusion protein in a cell, the fusion protein comprising the zinc finger binding domain and two FokI cleavage half-domains, wherein one of the cleavage half-domains comprises an alteration in amino acid 490 of the wild-type dimerization interface of the cleavage half-domain; and (c) contacting the cell with a polynucleotide comprising a third nucleotide sequence, wherein the third nucleotide sequence is homologous but non-identical with the first nucleotide sequence; wherein the fusion protein binds to the second sequence and cleaves the cellular chromatin in the region of interest, thereby facilitating homologous recombination between the first nucleotide sequence and the third nucleotide sequence, resulting in alteration of the first nucleotide sequence.
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30. A method for altering a first nucleotide sequence in a region of interest in cellular chromatin in an isolated cell, the method comprising:
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(a) engineering a first zinc finger binding domain to bind to a second nucleotide sequence in the region of interest, wherein the second sequence comprises at least 9 nucleotides; (b) providing a second zinc finger binding domain to bind to a third nucleotide sequence, wherein the third sequence comprises at least 9 nucleotides and is located between 2 and 50 nucleotides from the second sequence; (c) constitutively expressing a first fusion protein in a cell, the first fusion protein comprising the first zinc finger binding domain and a first FokI cleavage half-domain; and (d) constitutively expressing a second fusion protein in the cell, the second fusion protein comprising the second zinc finger binding domain and a second FokI cleavage half domain, wherein one of the cleavage half-domains comprises an alteration in amino acid 490 of the wild-type dimerization interface of the cleavage half-domain; wherein the first fusion protein binds to the second sequence, and the second fusion protein binds to the third sequence, thereby positioning the cleavage half-domains such that the cellular chromatin is cleaved at a cleavage site in the first nucleotide sequence, and non-homologous end joining at the cleavage site results in alteration of the first nucleotide sequence. - View Dependent Claims (31, 32, 33, 34, 35, 36, 37, 38)
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Specification