Sự biến đổi Histone: Từ bản đồ toàn bộ bộ gen đến những hiểu biết chức năng

Peterson CL, Laniel MA: Histones and histone modifications. Curr Biol. 2004, 14: R546-R551. 10.1016/j.cub.2004.07.007. Khorasanizadeh S: The nucleosome: from genomic organization to genomic regulation. Cell. 2004, 116: 259-272. 10.1016/S0092-8674(04)00044-3. Brehm A, Tufteland KR, Aasland R, Becker PB: The many colours of chromodomains. BioEssays. 2004, 26: 133-140. 10.1002/bies.10392. Zeng L, Zhou MM: Bromodomain: an acetyl-lysine binding domain. FEBS Lett. 2002, 513: 124-128. 10.1016/S0014-5793(01)03309-9. Carmen AA, Milne L, Grunstein M: Acetylation of the yeast histone H4 N terminus regulates its binding to heterochromatin protein SIR3. J Biol Chem. 2002, 277: 4778-4781. 10.1074/jbc.M110532200. Bernstein BE, Humphrey EL, Liu CL, Schreiber SL: The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modifications. Methods Enzymol. 2004, 376: 349-360. Robyr D, Kurdistani SK, Grunstein M: Analysis of genome-wide histone acetylation state and enzyme binding using DNA microarrays. Methods Enzymol. 2004, 376: 289-304. Lee CK, Shibata Y, Rao B, Strahl BD, Lieb JD: Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat Genet. 2004, 36: 900-905. 10.1038/ng1400. Bernstein BE, Liu CL, Humphrey EL, Perlstein EO, Schreiber SL: Global nucleosome occupancy in yeast. Genome Biol. 2004, 5: R62-10.1186/gb-2004-5-9-r62. Roh TY, Ngau WC, Cui K, Landsman D, Zhao K: High-resolution genome-wide mapping of histone modifications. Nat Biotechnol. 2004, 22: 1013-1016. 10.1038/nbt990. Reinke H, Horz W: Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol Cell. 2003, 11: 1599-1607. 10.1016/S1097-2765(03)00186-2. Boeger H, Griesenbeck J, Strattan JS, Kornberg RD: Nucleosomes unfold completely at a transcriptionally active promoter. Mol Cell. 2003, 11: 1587-1598. 10.1016/S1097-2765(03)00231-4. Kurdistani SK, Tavazoie S, Grunstein M: Mapping global histone acetylation patterns to gene expression. Cell. 2004, 117: 721-733. 10.1016/j.cell.2004.05.023. Schübeler D, MacAlpine DM, Scalzo D, Wirbelauer C, Kooperberg C, van Leeuwen F, Gottschling DE, O'Neill LP, Turner BM, Delrow J, et al: The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev. 2004, 18: 1263-1271. 10.1101/gad.1198204. Hanlon SE, Lieb JD: Progress and challenges in profiling the dynamics of chromatin and transcription factor binding with DNA microarrays. Curr Opin Genet Dev. 2004, 14: 697-705. 10.1016/j.gde.2004.09.008. Wei Y, Yu L, Bowen J, Gorovsky MA, Allis CD: Phosphorylation of histone H3 is required for proper chromosome condensation and segregation. Cell. 1999, 97: 99-109. 10.1016/S0092-8674(00)80718-7. Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, McMahon S, Karlsson EK, Kulbokas EJ, Gingeras TR, et al: Genomic maps and comparative analysis of histone modifications in human and mouse. Cell. 2005, 120: 169-181. 10.1016/j.cell.2005.01.001. Robyr D, Suka Y, Xenarios I, Kurdistani SK, Wang A, Suka N, Grunstein M: Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell. 2002, 109: 437-446. 10.1016/S0092-8674(02)00746-8. Robert F, Pokholok DK, Hannett NM, Rinaldi NJ, Chandy M, Rolfe A, Workman JL, Gifford DK, Young RA: Global position and recruitment of HATs and HDACs in the yeast genome. Mol Cell. 2004, 16: 199-209. 10.1016/j.molcel.2004.09.021. Wang A, Kurdistani SK, Grunstein M: Requirement of Hos2 histone deacetylase for gene activity in yeast. Science. 2002, 298: 1412-1414. 10.1126/science.1077790. Dion MF, Altschuler SJ, Wu LF, Rando OJ: Genomic characterization reveals a simple histone H4 acetylation code. Proc Natl Acad Sci USA. 2005, 102: 5501-5506. 10.1073/pnas.0500136102. Suka N, Suka Y, Carmen AA, Wu J, Grunstein M: Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin. Mol Cell. 2001, 8: 473-479. 10.1016/S1097-2765(01)00301-X. Smith ST, Petruk S, Sedkov Y, Cho E, Tillib S, Canaani E, Mazo A: Modulation of heat shock gene expression by the TAC1 chromatin-modifying complex. Nat Cell Biol. 2004, 6: 162-167. 10.1038/ncb1088. Gerber M, Shilatifard A: Transcriptional elongation by RNA polymerase II and histone methylation. J Biol Chem. 2003, 278: 26303-26306. 10.1074/jbc.R300014200. Wang H, Huang ZQ, Xia L, Feng Q, Erdjument-Bromage H, Strahl BD, Briggs SD, Allis CD, Wong J, Tempst P, et al: Methylation of histone H4 at arginine 3 facilitating transcriptional activation by nuclear hormone receptor. Science. 2001, 293: 853-857. 10.1126/science.1060781. Schreiber SL, Bernstein BE: Signaling network model of chromatin. Cell. 2002, 111: 771-778. 10.1016/S0092-8674(02)01196-0. Santos-Rosa H, Schneider R, Bernstein BE, Karabetsou N, Morillon A, Weise C, Schreiber SL, Mellor J, Kouzarides T: Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin. Mol Cell. 2003, 12: 1325-1332. 10.1016/S1097-2765(03)00438-6. Ng HH, Robert F, Young RA, Struhl K: Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell. 2003, 11: 709-719. 10.1016/S1097-2765(03)00092-3. Morillon A, Karabetsou N, O'Sullivan J, Kent N, Proudfoot N, Mellor J: Isw1 chromatin remodeling ATPase coordinates transcription elongation and termination by RNA polymerase II. Cell. 2003, 115: 425-435. 10.1016/S0092-8674(03)00880-8. Kurdistani SK, Robyr D, Tavazoie S, Grunstein M: Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nat Genet. 2002, 31: 248-254. 10.1038/ng907. Humphrey EL, Shamji AF, Bernstein BE, Schreiber SL: Rpd3p relocation mediates a transcriptional response to rapamycin in yeast. Chem Biol. 2004, 11: 295-299. 10.1016/j.chembiol.2004.03.001. Schwartz YB, Kahn TG, Pirrotta V: Characteristic low density and shear sensitivity of cross-linked chromatin containing polycomb complexes. Mol Cell Biol. 2005, 25: 432-439. 10.1128/MCB.25.1.432-439.2005. van Steensel B, Delrow J, Henikoff S: Chromatin profiling using targeted DNA adenine methyltransferase. Nat Genet. 2001, 27: 304-308. 10.1038/85871. Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, et al: Role of transposable elements in heterochromatin and epigenetic control. Nature. 2004, 430: 471-476. 10.1038/nature02651. Beer MA, Tavazoie S: Predicting gene expression from sequence. Cell. 2004, 117: 185-198. 10.1016/S0092-8674(04)00304-6.