H2A.Z-mediated genome-wide chromatin specialization

Current Genomics

Volumn 8, Issue 1, 2007, Pages 59-66

  Eirin Lopez J M ^a,b   Ausio J ^a  

^a UNIVERSITY OF VICTORIA   (Canada)

^b UNIVERSITY OF A CORUÑA   (Spain)

Author keywords

Acetylation; Gene activity; Genome wide distribution; H2A.Z; Heterochromatin; Promoter regions

Indexed keywords

DNA DIRECTED RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE III; HISTONE ACETYLTRANSFERASE GCN5; HISTONE DEACETYLASE; HISTONE H2A; HISTONE H2AX; HISTONE H2AZ; HISTONE H4; NUCLEAR PROTEIN; UNCLASSIFIED DRUG;

ACETYLATION; AMINO TERMINAL SEQUENCE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN IMMUNOPRECIPITATION; CHROMATIN STRUCTURE; CHROMOSOME STRUCTURE; DNA PACKAGING; DNA RECOMBINATION; DNA REPAIR; EUCHROMATIN; GENE EXPRESSION REGULATION; GENE LOCUS; GENE MUTATION; HETEROCHROMATIN; HUMAN; NONHUMAN; OPEN READING FRAME; PROMOTER REGION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROCESSING; REVIEW; TATA BOX; TRANSCRIPTION REGULATION;

EID: 33947650501     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920207780076965     Document Type: Review

References (39)

1. Malik, H.S. and Henikoff, S. Phylogenomics of the nucleosome. Nat. Struct. Biol., 2003, 10: 882-891.
2. Jenuwein, T. and Allis, C.D. Translating the histone code. Science, 2001, 293: 1074-1080.
3. Owen-Hughes, T. Colworth memorial lecture. Pathways for remodelling chromatin. Biochem. Soc. Trans., 2003, 31: 893-905.
4. Meneghini, M.D., Wu, M. and Madhani, H.D. Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell, 2003, 112: 725-736.
5. Dryhurst, D.D., Thambirajah, A.A. and Ausió, J. New twists on H2A.Z: a histone variant with a controversial structural and functional past. Biochem. Cell Biol., 2004, 82: 490-497.
6. Calestagne-Morelli, A. and Ausio, J. Long-range histone acetylation: biological significance, structural implications, and mechanisms. Biochem. Cell Biol., 2006, 84: 518-527.
7. Kimura, A., Umehara, T. and Horikoshi, M. Chromosomal gradient of histone acetylation established by Sas2p and Sir2p functions as a shield against gene silencing. Nat. Genet., 2002, 32: 370-377.
8. Suka, N., Luo, K. and Grunstein, M. Sir2p and Sas2p opposingly regulate acetylation of yeast histone H4 lysine 16 and spreading of heterochromatin. Nat. Genet., 2002, 32: 378-383.
9. Ng, H.H., Ciccione, D.N., Morshead, K.B., Oettinger, M.A. and Struhl, K. Lysine-79 of histone H3 is hypomethylated at silenced loci in yeast and mammalian cells: a potential mechanism for position-effect variegation. Proc. Natl. Acad. Sci. U.S.A., 2003, 100: 1820-1825.
10. Santos-Rosa, H., Bannister, A.J., Dehe, P.M., Geli, V. and Kouzarides, T. Methylation of H3 lysine 4 at euchromatin promotes Sir3p association with heterochromatin. J. Biol. Chem., 2004, 279: 47506-47512.
11. Bruce, K., Myers, F.A., Mantouvalou, E., Lefevre, P., Greaves, I., Bonifer, C., Tremethick, D.J., Thorne, A.W. and Crane-Robinson, C. The replacement histone H2A.Z in hyperacetylated form is a feature of active genes in chicken. Nucl. Acids Res., 2005, 33: 5633-5639.
12. Larochelle, M. and Gaudreau, L. H2A.Z has a function reminiscent of an activator required for preferential binding to intergenic DNA. EMBO J., 2003, 22: 4512-4522.
13. Santisteban, M.S., Kalashnikova, T. and Smith, M.M. Histone H2A.Z regulates transcription and is partially redundant with nucleosome remodeling complexes. Cell, 2000, 103: 411-422.
14. Krogan, N.J., Baetz, K., Keogh, M.-C., Datta, N., Sawa, C., Kwok, T.C., Thompson, N.J., Davey, M.G., Pootoolal, J., Hughes, T.R., Emili, A., Buratowski, S., Hieter, P. and Greenblatt, J.F. Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4. Proc. Natl. Acad. Sci. U.S.A., 2004, 101: 13513-13518.
15. Dhillon, N., Oki, M., Szyjka, S.J., Aparicio, O.M. and Kamakaka, R.T. H2A.Z functions to regulate progression through the cel cycle. Mol. Cell. Biol., 2006, 26: 489-501.
16. Raisner, R.M., Hartley, P.D., Meneghini, M.D., Bao, M.Z., Liu, C.L., Schreiber, S.L., Rando, O.J. and Madhani, H.D. Histone variant H2A.Z.marks the 5′ ends of both active and inactive genes in euchromatin. Cell, 2005, 123: 233-248.
17. Zhang, H., Roberts, D.N. and Cairns, B.R. Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss. Cell, 2005, 123: 219-231.
18. Kobor, M.S., Venkatasubrahmanyam, S., Meneghini, M.D., Gin, J.W., Jennings, J.L., Link, A.J., Madhani, H.D. and Rine, J. A protein complex containing the conserved Swi1/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol., 2004, 2: E131.
19. Krogan, N.J., Keogh, M.-C., Datta, N., Sawa, C., Ryan, O.W., Ding, H., Haw, R.A., Pootoolal, J., Tong, A., Canadien, V., Richards, D.P., Wu, X., Emili, A., Hughes, T.R., Buratowski, S. and Greenblatt, J.F. A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol. Cell, 2003, 12: 1565-1576.
20. Mizuguchi, G., Shen, X., Landry, J., Hu, W.-H., Sen, S. and Wu, C. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science, 2004, 303: 343-348.
21. Yuan, G.C., Liu, Y.J., Dion, M.F., Slack, M.D., Wu, L.F., Altschuler, S.J. and Rando, O.J. Genome-scale identification of nucleosome positions in S. cerevisiae. Science, 2005, 309: 626-630.
22. Millar, C.B., Xu, F., Zhang, K. and Grunstein, M. Acetylation of H2AZ Lys 14 is associated with genome-wide gene activity in yeast. Genes Dev., 2006, 20: 711-722.
23. Thambirajah, A.A., Dryhurst, D.D., Ishibashi, T., Li, A., Maffey, A.H. and Ausio, J. H2A.Z sabilizes chromatin in a way that is dependent on core histone acetylation. J. Biol. Chem., 2005, 281: 20036-20044.
24. Farris, S.D., Rubio, E.D., Moon, J.J., Gombert, W.M., Nelson, B.H. and Krumm, A. Transcription-induced chromatin remodeling at the c-myc gene involves the local exchange of histone H2A.Z. J. Biol. Chem., 2005, 280: 25298-25303.
25. Bernstein, B.E., Liu, C.L., Humphrey, E.L., Perlstein, E.O. and Schreiber, S.L. Global nucleosome occupancy in yeast. Genome Biol., 2004, 5: R62.
26. Lee, C.K., Shibata, Y., Rao, B., Strahl, B.D. and Lieb, J.D. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat. Genet., 2004, 36: 900-905.
27. Babiarz, J.E., Halley, J.E. and Rine, J. Telomeric heterochromatin boundaries require NuA4-dependent acetylation of histone variant H2A.Z in Saccharomyces cerevisiae. Genes Dev., 2006, 20: 700-710.
28. Keogh, M.-C., Mennella, T.A., Sawa, C., Berthelet, S., Krogan, N.J., Wolek, A., Podolny, V., Carpenter, L.R., Greenblatt, J.F., Baetz, K. and Buratowski, S. The Saccharomyces cerevisiae histone H2A variant Htz1 is acetylated by NuA4. Genes Dev., 2006, 20: 660-665.
29. Redon, C., Pilch, D., Rogakou, E., Sedelnikova, O., Newrock, K. and Bonner, W. Histone H2A variants H2A.X and H2A.Z. Curr. Opin. Genet. Dev., 2002, 12: 162-169.
30. Jackson, J.D. and Gorovsky, M.A. Histone H2A.Z has a conserved function that is distinct from that of the major H2A sequence variants. Nucl. Acids Res., 2000, 28: 3811-3816.
31. Wu, W.H., Alami, S., Luk, E., Wu, C.H., Sen, S., Mizuguchi, G., Wei, D. and Wu, C. Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange. Nat. Struct. Mol. Biol., 2005, 12: 1064-1071.
32. Kurdistani, S.K., Tavazoie, S. and Grunstein, M. Mapping global hisone acetylation patterns to gene expression. Cell, 2004, 117: 721-733.
33. Liu, C.L., Kaplan, T., Kim, M., Buratowski, S., Schreiber, S.L., Friedman, N. and Rando, O.J. Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol., 2005, 3: E328.
34. Elemento, O. and Tavazoie, S. Fast and sysematic genome-wide discovery of conserved regulatory elements using a non-aligment based approach. Genome Biol., 2005, 6: R18.
35. Cai, Y., Jin, J., Tomomori-Sato, C., Sato, S., Sorokina, I., Parmely, T.J., Conaway, R.C. and Conaway, J.W. Identification of new subunits of the multprotein mammalian TRRAP/TIP60-containing histone acetyltransferase complex. J. Biol. Chem., 2003, 278: 42733-42736.
36. Doyon, Y., Selleck, W., Lane, W.S., Tan, S. and Cote, J. Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeast to humans. Mol. Cell. Biol., 2004, 24: 1884-1896.
37. Zhang, H., Richardson, D.O., Roberts, D.N., Utley, R., Erdjument-Bromage, H., Tempst, P., Cote, J. and Cairns, B.R. The Yaf9 component of the SWR1 and NuA4 complexes is required for proper gene expression, histone H4 acetylation, and Htz1 replacement near telomeres. Mol. Cell. Biol., 2004, 24: 9424-9436.
38. Ausió, J. Histone variants: the structure behind the function. Brief. Funct. Genomic. Proteomic., 2006, 5: 228-243.
39. Grunstein, M. Molecular model for telomeric heterochromatin in yeast. Curr. Opin. Cell Biol., 1997, 9: 383-387.