Patterning chromatin: Form and function for H2A.Z variant nucleosomes

Current Opinion in Genetics and Development

Volumn 16, Issue 2, 2006, Pages 119-124

  Raisner, Ryan M ^a   Madhani, Hiten D ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H2A; PROTEIN HISTONE H2A Z; UNCLASSIFIED DRUG;

ACETYLATION; CENTROMERE; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMOSOMAL INSTABILITY; EUCHROMATIN; EUKARYOTE; GENE ACTIVATION; GENE SILENCING; HETEROCHROMATIN; HUMAN; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN FUNCTION; REVIEW; SACCHAROMYCES CEREVISIAE; SPECIES COMPARISON; TRANSCRIPTION INITIATION SITE;

ANIMALS; CHROMATIN; HISTONES; NUCLEOSOMES; VARIATION (GENETICS);

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 33644850957     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2006.02.005     Document Type: Review

References (38)

1. T.H. Thatcher, and M.A. Gorovsky Phylogenetic analysis of the core histones H2A, H2B, H3, and H4 Nucleic Acids Res 22 1994 174 179
2. C. Costanzi, and J.R. Pehrson Histone macroH2A1 is concentrated in the inactive X chromosome of female mammals Nature 393 1998 599 601
3. T. Gautier, D.W. Abbott, A. Molla, A. Verdel, J. Ausio, and S. Dimitrov Histone variant H2ABbd confers lower stability to the nucleosome EMBO Rep 5 2004 715 720
4. C. Redon, D.R. Pilch, E.P. Rogakou, A.H. Orr, N.F. Lowndes, and W.M. Bonner Yeast histone 2A serine 129 is essential for the efficient repair of checkpoint-blind DNA damage EMBO Rep 4 2003 678 684
5. J.D. Jackson, and M.A. Gorovsky Histone H2A.Z has a conserved function that is distinct from that of the major H2A sequence variants Nucleic Acids Res 28 2000 3811 3816
6. A.M. Carr, S.M. Dorrington, J. Hindley, G.A. Phear, S.J. Aves, and P. Nurse Analysis of a histone H2A variant from fission yeast: evidence for a role in chromosome stability Mol Gen Genet 245 1994 628 635
7. T.J. Leach, M. Mazzeo, H.L. Chotkowski, J.P. Madigan, M.G. Wotring, and R.L. Glaser Histone H2A.Z is widely but nonrandomly distributed in chromosomes of Drosophila melanogaster J Biol Chem 275 2000 23267 23272
8. C.D. Allis, R. Richman, M.A. Gorovsky, Y.S. Ziegler, B. Touchstone, W.A. Bradley, and R.G. Cook hv1 is an evolutionarily conserved H2A variant that is preferentially associated with active genes J Biol Chem 261 1986 1941 1948
9. R.P. Harvey, J.A. Whiting, L.S. Coles, P.A. Krieg, and J.R. Wells H2A.F: an extremely variant histone H2A sequence expressed in the chicken embryo Proc Natl Acad Sci USA 80 1983 2819 2823
10. S.G. Ernst, H. Miller, C.A. Brenner, C. Nocente-McGrath, S. Francis, R. McIsaac, R.P. Harvey, J.A. Whiting, L.S. Coles, and P.A. Krieg Characterization of a cDNA clone coding for a sea urchin histone H2A variant related to the H2A.F/Z histone protein in vertebrates Nucleic Acids Res 15 1987 4629 4644
11. R.K. Suto, M.J. Clarkson, D.J. Tremethick, and K. Luger Crystal structure of a nucleosome core particle containing the variant histone H2A.Z Nat Struct Biol 7 2000 1121 1124
12. D.W. Abbott, V.S. Ivanova, X. Wang, W.M. Bonner, and J. Ausio Characterization of the stability and folding of H2A.Z chromatin particles: implications for transcriptional activation J Biol Chem 276 2001 41945 41949
13. Y.J. Park, P.N. Dyer, D.J. Tremethick, and K. Luger A new fluorescence resonance energy transfer approach demonstrates that the histone variant H2AZ stabilizes the histone octamer within the nucleosome J Biol Chem 279 2004 24274 24282
14. A. Flaus, C. Rencurel, H. Ferreira, N. Wiechens, and T. Owen-Hughes Sin mutations alter inherent nucleosome mobility EMBO J 23 2004 343 353
15. H. Zhang, D.N. Roberts, and B.R. Cairns Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss Cell 123 2005 219 231 The authors localize H2A.Z across the yeast genome at the resolution of intergenic regions and open reading frames. A selective enrichment of promoter segments with H2A.Z was found, and this negatively correlated with transcription. On the basis of this observation and the sensitivity of H2A.Z to salt extraction in isolated yeast chromatin, the authors propose that H2A.Z facilitates nucleosome loss during gene induction.
16. L.A. Stargell, J. Bowen, C.A. Dadd, P.C. Dedon, M. Davis, R.G. Cook, C.D. Allis, and M.A. Gorovsky Temporal and spatial association of histone H2A variant hv1 with transcriptionally competent chromatin during nuclear development in Tetrahymena thermophila Genes Dev 7 1993 2641 2651
17. R.M. Raisner, P.D. Hartley, M.D. Meneghini, M.Z. Bao, C.L. Liu, S.L. Schreiber, O.J. Rando, and H.D. Madhani Histone variant H2A.Z marks the 5′ ends of both active and inactive genes in euchromatin Cell 123 2005 233 248 Using chromatin immunoprecipitation and high-density tiling microarrays, the authors demonstrate that two H2A.Z nucleosomes flank a nucleosome-free region at the transcription start site of most genes in yeast euchromatin. This localization is dependent upon histone acetylation and Bdf1 but does not require gene transcription. A 22 bp segment containing a binding site for the Myb-related protein Reb1 and an adjacent dA:dT tract was shown to be sufficient to induce a nucleosome-free region flanked by two H2A.Z nucleosomes.
18. B. Guillemette, A.R. Bataille, N. Gevry, M. Adam, M. Blanchette, F. Robert, and L. Gaudreau Variant histone H2A.Z Is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning PLoS Biol 3 2005 e384 To demonstrate promoter enrichment with H2A.Z, the authors immunoprecipated sonicated S. cerevisiae chromatin with anti-Myc-H2A.Z antibodies and hybridized probes derived from this material to microarrays that contain an oligonucleotide approximately every 300 bp across the genome. Additionally, they used indirect end-labeled micrococcal nuclease-digested DNA to show that there is a small shift in the position of nucleosomes at the GAL1 promoter in an htz1Δ strain.
19. J.P. Madigan, H.L. Chotkowski, and R.L. Glaser DNA double-strand break-induced phosphorylation of Drosophila histone variant H2Av helps prevent radiation-induced apoptosis Nucleic Acids Res 30 2002 3698 3705
20. K. Bruce, F.A. Myers, E. Mantouvalou, P. Lefevre, I. Greaves, C. Bonifer, D.J. Tremethick, A.W. Thorne, and C. Crane-Robinson The replacement histone H2A.Z in a hyperacetylated form is a feature of active genes in the chicken Nucleic Acids Res 33 2005 5633 5639 The authors use chromatin immunoprecipitation for both acetylated and unacetylated forms of H2A.Z in chicken to show that the 5′ ends of both tissue-specific and housekeeping genes are selectively enriched with the acetylated form. Notably, the β-globin insulator element is highly enriched with acetylated H2A.Z.
21. D. Rangasamy, L. Berven, P. Ridgway, and D.J. Tremethick Pericentric heterochromatin becomes enriched with H2A.Z during early mammalian development EMBO J 22 2003 1599 1607
22. D. Rangasamy, I. Greaves, and D.J. Tremethick RNA interference demonstrates a novel role for H2A.Z in chromosome segregation Nat Struct Mol Biol 11 2004 650 655 The authors use an inducible RNAi system to demonstrate that H2A.Z is required for proper segregation of chromosomes in mammalian cells.
23. G. Mizuguchi, X. Shen, J. Landry, W.H. Wu, S. Sen, and C. Wu ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex Science 303 2004 343 348 The authors demonstrate using in vitro and in vivo assays that a complex containing the Swi2/Snf2-related ATPase Swr1 is responsible for H2A.Z deposition in yeast.
24. N.J. Krogan, M.C. Keogh, N. Datta, C. Sawa, O.W. Ryan, H. Ding, R.A. Haw, J. Pootoolal, A. Tong, and V. Canadien A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1 Mol Cell 12 2003 1565 1576
25. M.S. Kobor, S. Venkatasubrahmanyam, M.D. Meneghini, J.W. Gin, J.L. Jennings, A.J. Link, H.D. Madhani, and J. Rine A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin PLoS Biol 2 2004 E131 The authors purify the 13-subunit Swr1-C in yeast and demonstrate that it is required for in vivo deposition of H2A.Z.
26. T. Kusch, L. Florens, W.H. Macdonald, S.K. Swanson, R.L. Glaser, J.R. Yates III, S.M. Abmayr, M.P. Washburn, and J.L. Workman Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions Science 306 2004 2084 2087 The authors demonstrate that the Drosophila Tip60 complex is responsible for acetylation and exchange of the phosphorylated H2Av histone variant with unphosphorylated H2Av at sites of DNA lesions.
27. Y. Cai, J. Jin, L. Florens, S.K. Swanson, T. Kusch, B. Li, J.L. Workman, M.P. Washburn, R.C. Conaway, and J.W. Conaway The mammalian YL1 protein is a shared subunit of the TRRAP/TIP60 histone acetyltransferase and SRCAP complexes J Biol Chem 280 2005 13665 13670 The authors purify a mammalian presumptive H2A.Z deposition complex and show that it has subunits homologous to those in the yeast Swr1-C and Drosophila Tip60 complexes.
28. M.S. Santisteban, T. Kalashnikova, and M.M. Smith Histone H2A.Z regulats transcription and is partially redundant with nucleosome remodeling complexes Cell 103 2000 411 422
29. M. Adam, F. Robert, M. Larochelle, and L. Gaudreau H2A.Z is required for global chromatin integrity and for recruitment of RNA polymerase II under specific conditions Mol Cell Biol 21 2001 6270 6279
30. N. Dhillon, M. Oki, S.J. Szyjka, O.M. Aparicio, and R.T. Kamakaka H2A.Z functions to regulate progression through the cell cycle Mol Cell Biol 26 2006 489 501
31. M.D. Meneghini, M. Wu, and H.D. Madhani Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin Cell 112 2003 725 736
32. A. van Daal, and S.C. Elgin A histone variant, H2AvD, is essential in Drosophila melanogaster Mol Biol Cell 3 1992 593 602
33. R. Faast, V. Thonglairoam, T.C. Schulz, J. Beall, J.R. Wells, H. Taylor, K. Matthaei, P.D. Rathjen, D.J. Tremethick, and I. Lyons Histone variant H2A.Z is required for early mammalian development Curr Biol 11 2001 1183 1187
34. J. Swaminathan, E.M. Baxter, and V.G. Corces The role of histone H2Av variant replacement and histone H4 acetylation in the establishment of Drosophila heterochromatin Genes Dev 19 2005 65 76
35. P. Ridgway, K.D. Brown, D. Rangasamy, U. Svensson, and D.J. Tremethick Unique residues on the H2A.Z containing nucleosome surface are important for Xenopus laevis development J Biol Chem 279 2004 43815 43820 Using immunofluorescence, RNAi and mutant alleles, the authors show that H2A.Z is localized in a tissue-specific manner and is required for proper Xenopus laevis development.
36. L.N. Rusche, A.L. Kirchmaier, and J. Rine The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae Annu Rev Biochem 72 2003 481 516
37. W.H. Wu, S. Alami, E. Luk, C.H. Wu, S. Sen, G. Mizuguchi, D. Wei, and C. Wu Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange Nat Struct Mol Biol 12 2005 1064 1071
38. B. Li, S.G. Pattenden, D. Lee, J. Gutierrez, J. Chen, C. Seidel, J. Gerton, and J.L. Workman Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling Proc Natl Acad Sci USA 102 2005 18385 18390