Variant histone H2A.z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning

PLoS Biology

Volumn 3, Issue 12, 2005, Pages 1-11

  Guillemette, Benoît ^a   Bataille, Alain R ^b   Gévry, Nicolas ^a   Adam, Maryse ^a   Blanchette, Mathieu ^c   Robert, François ^b   Gaudreau, Luc ^a  

^a UNIVERSITÉ DE SHERBROOKE   (Canada)

^b CLIN RESEARCH INSTITUTE OF MONTREAL   (Canada)

^c MCGILL UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; CHROMATIN; CHROMOSOME ANALYSIS; CONTROLLED STUDY; DNA MICROARRAY; GENE CONTROL; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCATION; GENE LOCUS; GENE MAPPING; GENE SILENCING; GENETIC VARIABILITY; NONHUMAN; NUCLEOSOME; NUCLEOTIDE SEQUENCE; YEAST; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GENOME; METABOLISM; PROMOTER REGION; SACCHAROMYCES CEREVISIAE;

EUKARYOTA;

GENE EXPRESSION REGULATION, FUNGAL; GENOME, FUNGAL; HISTONES; NUCLEOSOMES; PROMOTER REGIONS (GENETICS); SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION, GENETIC; VARIATION (GENETICS);

EID: 29144531244     PISSN: 15457885     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.0030384     Document Type: Article

References (63)

1. Khorasanizadeh S (2004) The nucleosome: From genomic organization to genomic regulation. Cell 116: 259-272.
2. Vaquero A, Loyola A, Reinberg D (2003) The constantly changing face of chromatin. Sci Aging Knowledge Environ 2003: RE4.
3. Felsenfeld G, Groudine M (2003) Controlling the double helix. Nature 421: 448-453.
4. Flaus A, Owen-Hughes T (2004) Mechanisms for ATP-dependent chromatin remodelling: Farewell to the tuna-can octamer? Curr Opin Genet Dev 14: 165-173.
5. Lusser A, Kadonaga JT (2003) Chromatin remodeling by ATP-dependent molecular machines. Bioessays 25: 1192-1200.
6. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293: 1074-1080.
7. Turner BM (2002) Cellular memory and the histone code. Cell 111: 285-291.
8. Kamakaka RT, Biggins S (2005) Histone variants: Deviants? Genes Dev 19: 295-316.
9. Henikoff S, Ahmad K (2005) Assembly of variant histones into chromatin. Annu Rev Cell Dev Biol. In press.
10. Thatcher TH, Gorovsky MA (1994) Phylogenetic analysis of the core histones H2A, H2B, H3, and H4. Nucleic Acids Res 22: 174-179.
11. Wu RS, Nishioka D, Bonner WM (1982) Differential conservation of histone 2A variants between mammals and sea urchins. J Cell Biol 93: 426-431.
12. Liu X, Li B, Gorovsky MA (1996) Essential and nonessential histone H2A variants in Tetrahymena thermophila. Mol Cell Biol 16: 4305-4311.
13. Ridgway P, Brown KD, Rangasamy D, Svensson U, Tremethick DJ (2004) Unique residues on the H2A.Z containing nucleosome surface are important for Xenopus laevis development. J Biol Chem 279: 43815-43820.
14. Faast R, Thonglairoam V, Schulz TC, Beall J, Wells JR, et al. (2001) Histone variant H2A.Z is required for early mammalian development. Curr Biol 11: 1183-1187.
15. Wu RS, Bonner WM (1981) Separation of basal histone synthesis from Sphase histone synthesis in dividing cells. Cell 27: 321-330.
16. Redon C, Pilch D, Rogakou E, Sedelnikova O, Newrock K, et al. (2002) Histone H2A variants H2AX and H2AZ. Curr Opin Genet Dev 12: 162-169.
17. Jackson JD, Gorovsky MA (2000) Histone H2A.Z has a conserved function that is distinct from that of the major H2A sequence variants. Nucleic Acids Res 28: 3811-3816.
18. Clarkson MJ, Wells JR, Gibson F, Saint R, Tremethick DJ (1999) Regions of variant histone His2AvD required for Drosophila development. Nature 399: 694-697.
19. Adam M, Robert F, Larochelle M, Gaudreau L (2001) H2A.Z is required for global chromatin integrity and for recruitment of RNA polymerase II under specific conditions. Mol Cell Biol 21: 6270-6279.
20. Allis CD, Glover CV, Bowen JK, Gorovsky MA (1980) Histone variants specific to the transcriptionally active, amitotically dividing macronucleus of the unicellular eucaryote, Tetrahymena thermophila. Cell 20: 609-617.
21. Santisteban MS, Kalashnikova T, Smith MM (2000) Histone H2A.Z regulates transcription and is partially redundant with nucleosome remodeling complexes. Cell 103: 411-422.
22. Larochelle M, Gaudreau L (2003) H2A.Z has a function reminiscent of an activator required for preferential binding to intergenic DNA. EMBO J 22: 4512-4522.
23. Farris SD, Rubio ED, Moon JJ, Gombert WM, Nelson BH, et al. (2005) Transcription-induced chromatin remodeling at the c-myc gene involves the local exchange of histone H2A.Z. J Biol Chem 280: 25298-25303.
24. Meneghini MD, Wu M, Madhani HD (2003) Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell 112: 725-736.
25. Swaminathan J, Baxter EM, Corces VG (2005) The role of histone H2Av variant replacement and histone H4 acetylation in the establishment of Drosophila heterochromatin. Genes Dev 19: 65-76.
26. Dhillon N, Kamakaka RT (2000) A histone variant, Htz1p, and a Sir1p-like protein, Esc2p, mediate silencing at HMR. Mol Cell 6: 769-780.
27. Fan JY, Rangasamy D, Luger K, Tremethick DJ (2004) H2A.Z alters the nucleosome surface to promote HP1alpha-mediated chromatin fiber folding. Mol Cell 16: 655-661.
28. Rangasamy D, Berven L, Ridgway P, Tremethick DJ (2003) Pericentric heterochromatin becomes enriched with H2A.Z during early mammalian development. EMBO J 22: 1599-1607.
29. Kobor MS, Venkatasubrahmanyam S, Meneghini MD, Gin JW, Jennings JL, et al. (2004) A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol 2: e131. DOI: 10.1371/journal.pbio.0020131
30. Krogan NJ, Keogh MC, Datta N, Sawa C, Ryan OW, et al. (2003) A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol Cell 12: 1565-1576.
31. Mizuguchi G, Shen X, Landry J, Wu WH, Sen S, et al. (2004) ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303: 343-348.
32. Krogan NJ, Baetz K, Keogh MC, Datta N, Sawa C, et al. (2004) 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 101: 13513-13518.
33. Rangasamy D, Greaves I, Tremethick DJ (2004) RNA interference demonstrates a novel role for H2A.Z in chromosome segregation. Nat Struct Mol Biol 11: 650-655.
34. Leach TJ, Mazzeo M, Chotkowski HL, Madigan JP, Wotring MG, et al. (2000) Histone H2A.Z is widely but nonrandomly distributed in chromosomes of Drosophila melanogaster. J Biol Chem 275: 23267-23272.
35. Suto RK, Clarkson MJ, Tremethick DJ, Luger K (2000) Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nat Struct Biol 7: 1121-1124.
36. Robert F, Pokholok DK, Hannett NM, Rinaldi NJ, Chandy M, et al. (2004) Global position and recruitment of HATs and HDACs in the yeast genome. Mol Cell 16: 199-209.
37. Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, et al. (2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309: 626-630.
38. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104.
39. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, et al. (2000) Genomewide location and function of DNA binding proteins. Science 290: 2306-2309.
40. Ng HH, Robert F, Young RA, Struhl K (2002) Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex. Genes Dev 16: 806-819.
41. Ng HH, Robert F, Young RA, Struhl K (2003) Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell 11: 709-719.
42. Reinke H, Horz W (2003) Histones are First hyperacetylated and then lose contact with the activated PHO5 promoter. Mol Cell 11: 1599-1607.
43. Lee CK, Shibata Y, Rao B, Strahl BD, Lieb JD (2004) Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat Genet 36: 900-905.
44. Boeger H, Griesenbeck J, Strattan JS, Kornberg RD (2003) Nucleosomes unfold completely at a transcriptionally active promoter. Mol Cell 11: 1587-1598.
45. Boeger H, Griesenbeck J, Strattan JS, Kornberg RD (2004) Removal of promoter nucleosomes by disassembly rather than sliding in vivo. Mol Cell 14: 667-673.
46. Schwabish MA, Struhl K (2004) Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II. Mol Cell Biol 24: 10111-10117.
47. Fedor MJ, Lue NF, Kornberg RD (1988) Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast. J Mol Biol 204: 109-127.
48. Fedor MJ, Kornberg RD (1989) Upstream activation sequence-dependent alteration of chromatin structure and transcription activation of the yeast GAL1-GAL10 genes. Mol Cell Biol 9: 1721-1732.
49. Fisher-Adams G, Grunstein M (1995) Yeast histone H4 and H3 N-termini have different effects on the chromatin structure of the GAL1 promoter. EMBO J 14: 1468-1477.
50. Axelrod JD, Reagan MS, Majors J (1993) GAL4 disrupts a repressing nucleosome during activation of GAL1 transcription in vivo. Genes Dev 7: 857-869.
51. Abbott DW, Ivanova VS, Wang X, Bonner WM, Ausio J (2001) Characterization of the stability and folding of H2A.Z chromatin particles: Implications for transcriptional activation. J Biol Chem 276: 41945-41949.
52. Fan JY, Gordon F, Luger K, Hansen JC, Tremethick DJ (2002) The essential histone variant H2A.Z regulates the equilibrium between different chromatin conformational states. Nat Struct Biol 9: 172-176.
53. Rusche LN, Kirchmaier AL, Rine J (2003) The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem 72: 481-516.
54. Grewal SI, Moazed D (2003) Heterochromatin and epigenetic control of gene expression. Science 301: 798-802.
55. Martinez-Campa C, Politis P, Moreau JL, Kent N, Goodall J, et al. (2004) Precise nucleosome positioning and the TATA box dictate requirements for the histone H4 tail and the bromodomain factor Bdf1. Mol Cell 15: 69-81.
56. Schneider BL, Seufert W, Steiner B, Yang QH, Futcher AB (1995) Use of polymerase chain reaction epitope tagging for protein tagging in Saccharomyces cerevisiae. Yeast 11: 1265-1274.
57. Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, et al. (2005) Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122: 517-527.
58. Drouin S, Robert F (2005) Genome-wide location analysis of chromatin-associated proteins by ChIP on CHIP: Controls matter. Methods. In press.
59. Svaren J, Venter U, Hörz W (1995) In vivo analysis of nucleosome structure and transcription factor binding in Saccharomyces cerevisiae. In: Methods in molecular genetics: Molecular microbiology techniques, Part B. New York: Academic Press. pp. 153-167
60. Lieb JD, Liu X, Botstein D, Brown PO (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28: 327-334.
61. Kurdistani SK, Tavazoie S, Grunstein M (2004) Mapping global histone acetylation patterns to gene expression. Cell 117: 721-733.
62. Wang B, Matsuoka S, Carpenter PB, Elledge SJ (2002) 53BP1, a mediator of the DNA damage checkpoint. Science 298: 1435-1438.
63. Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, et al. (1998) Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95: 717-728.