Methods and compositions for treating Huntington's Disease

1. A non-naturally occurring zinc finger protein that binds to an Htt gene, the zinc finger protein comprising 4, 5 or 6 zinc finger domains ordered F1 to F4, F1 to F5 and F1 to F6, wherein the zinc finger domains comprise the recognition helix regions sequences shown in a single row of Table 1B.

2. The zinc finger protein of claim 1 , wherein the zinc finger protein binds entirely or partially outside the CAG repeat region of the Htt gene.

3. The zinc finger protein of claim 1 , wherein the zinc finger protein binds to sequences within the CAG repeat region of the Htt gene.

4. The zinc finger protein of claim 1 , further comprising a dimerization domain that allows multimerization of zinc finger proteins when bound to DNA.

5. A fusion protein comprising a zinc finger protein of claim 1 and a functional domain, wherein the functional domain is selected from the group consisting of a transcriptional activation domain, a transcriptional repression domain, and a nuclease domain.

6. A polynucleotide encoding one or more zinc finger proteins of claim 1 .

7. A pharmaceutical composition comprising one or more polynucleotides according to claim 6 .

8. A host cell comprising one or more zinc finger proteins of claim 1 .

9. A pharmaceutical composition comprising one or more zinc finger proteins according to claim 1 .

10. A method of modifying expression of an Htt gene in a cell, the method comprising administering to the cell one or more polynucleotides encoding one or more fusion proteins according to claim 5 .

11. The method of claim 10 , wherein the Htt gene comprises at least one mutant allele.

12. The method of claim 10 , wherein the Htt gene is wild-type.

13. The method of claim 10 , wherein the fusion protein comprises a nuclease domain and expression of the Htt gene is inactivated.

14. A method of modifying an Htt gene in a cell, the method comprising, administering to the cell one or more polynucleotides encoding one or more fusion proteins according to claim 5 , wherein the one or more fusion proteins comprises a nuclease domain and wherein the sequence of the Htt gene is modified.

15. A method of generating a model system for the study of Huntington's Disease, the method comprising modifying an Htt gene according to the method of claim 14 .

16. The method of claim 15 , wherein the cell comprises an embryonic stem cell.

17. The method of claim 15 , wherein the Htt gene is modified to comprise one or more mutant alleles.

18. The method of claim 17 , wherein the mutant alleles comprise expanded trinucleotide repeats.

19. A method of treating Huntington's Disease, the method comprising administering one or more polynucleotides encoding one or more fusion proteins according to claim 5 to a subject in need thereof.