Genome-wide analysis of interactions between ATP-dependent chromatin remodeling and histone modifications

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Dai, Zhiming ^a   Dai, Xianhua ^a   Xiang, Qian ^a   Feng, Jihua ^a   Wang, Jiang ^a   Deng, Yangyang ^a   He, Caisheng ^a  

^a SUN YAT SEN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; HISTONE; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN STRUCTURE; CONTROLLED STUDY; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; MATHEMATICAL COMPUTING; MOLECULAR INTERACTION; NONHUMAN; PROTEIN MODIFICATION; SACCHAROMYCES CEREVISIAE; BINDING SITE; BIOLOGY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METHODOLOGY; NUCLEOSOME; PROTEIN PROCESSING;

SACCHAROMYCES CEREVISIAE;

ADENOSINE TRIPHOSPHATE; BINDING SITES; CHROMATIN ASSEMBLY AND DISASSEMBLY; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION, FUNGAL; HISTONES; NUCLEOSOMES; PROTEIN PROCESSING, POST-TRANSLATIONAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 67651238767     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-304     Document Type: Article

References (47)

1. Saha A Wittmeyer J Cairns BR Chromatin remodelling: The industrial revolution of DNA around histones Nat Rev Mol Cell Biol 2006, 7(6):437-447. 10.1038/nrm1945 16723979
2. Whitehouse I Rando OJ Delrow J Tsukiyama T Chromatin remodelling at promoters suppresses antisense transcription Nature 2007, 450(7172):1031-1035. 10.1038/nature06391 18075583
3. Kouzarides T Chromatin modifications and their function Cell 2007, 128(4):693-705. 10.1016/j.cell.2007.02.005 17320507
4. Shahbazian MD Grunstein M Functions of site-specific histone acetylation and deacetylation Annu Rev Biochem 2007, 76:75-100. 10.1146/ annurev.biochem.76.052705.162114 17362198
5. Ferreira H Flaus A Owen-Hughes T Histone modifications influence the action of Snf2 family remodelling enzymes by different mechanisms J Mol Biol 2007, 374(3):563-579. 2279226 17949749 10.1016/j.jmb.2007.09.059
6. Cosgrove MS Boeke JD Wolberger C Regulated nucleosome mobility and the histone code Nat Struct Mol Biol 2004, 11(11):1037-1043. 10.1038/nsmb851 15523479
7. Hassan AH Prochasson P Neely KE Galasinski SC Chandy M Carrozza MJ Workman JL Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes Cell 2002, 111(3):369-379. 10.1016/S0092-8674(02)01005-X 12419247
8. Bannister AJ Zegerman P Partridge JF Miska EA Thomas JO Allshire RC Kouzarides T Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain Nature 2001, 410(6824):120-124. 10.1038/ 35065138 11242054
9. Burgio G La Rocca G Sala A Arancio W Di Gesu D Collesano M Sperling AS Armstrong JA van Heeringen SJ Logie C et al Genetic identification of a network of factors that functionally interact with the nucleosome remodeling ATPase ISWI PLoS Genet 2008, 4(6):e1000089. 2390755 18535655 10.1371/journal.pgen.1000089
10. Ruthenburg AJ Li H Patel DJ Allis CD Multivalent engagement of chromatin modifications by linked binding modules Nat Rev Mol Cell Biol 2007, 8(12):983-994. 10.1038/nrm2298 18037899
11. O'Connor TR Wyrick JJ ChromatinDB: A database of genome-wide histone modification patterns for Saccharomyces cerevisiae Bioinformatics 2007, 23(14):1828-1830. 10.1093/bioinformatics/btm236 17485428
12. Pokholok DK Harbison CT Levine S Cole M Hannett NM Lee TI Bell GW Walker K Rolfe PA Herbolsheimer E et al Genome-wide map of nucleosome acetylation and methylation in yeast Cell 2005, 122(4):517-527. 10.1016/ j.cell.2005.06.026 16122420
13. Steinfeld I Shamir R Kupiec M A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription Nat Genet 2007, 39(3):303-309. 10.1038/ng1965 17325681
14. Venters BJ Pugh BF A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome Genome Res 2009, 19(3):360-371. 10.1101/gr.084970.108 19124666
15. Cairns BR Lorch Y Li Y Zhang M Lacomis L Erdjument-Bromage H Tempst P Du J Laurent B Kornberg RD RSC, an essential, abundant chromatin-remodeling complex Cell 1996, 87(7):1249-1260. 10.1016/S0092-8674(00)81820-6 8980231
16. Kasten M Szerlong H Erdjument-Bromage H Tempst P Werner M Cairns BR Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys14 Embo J 2004, 23(6):1348-1359. 381415 15014446 10.1038/ sj.emboj.7600143
17. Angus-Hill ML Schlichter A Roberts D Erdjument-Bromage H Tempst P Cairns BR A Rsc3/Rsc30 zinc cluster dimer reveals novel roles for the chromatin remodeler RSC in gene expression and cell cycle control Mol Cell 2001, 7(4):741-751. 10.1016/S1097-2765(01)00219-2 11336698
18. Raisner RM Hartley PD Meneghini MD Bao MZ Liu CL Schreiber SL Rando OJ Madhani HD Histone variant H2A.Z marks the 5' ends of both active and inactive genes in euchromatin Cell 2005, 123(2):233-248. 2039754 16239142 10.1016/j.cell.2005.10.002
19. Guillemette B Bataille AR Gevry N Adam M Blanchette M Robert F Gaudreau L Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning PLoS Biol 2005, 3(12):e384. 1275524 16248679 10.1371/journal.pbio.0030384
20. Hassan AH Awad S Al-Natour Z Othman S Mustafa F Rizvi TA Selective recognition of acetylated histones by bromodomains in transcriptional co-activators Biochem J 2007, 402(1):125-133. 1783998 17049045 10.1042/ BJ20060907
21. Topalidou I Papamichos-Chronakis M Thireos G Tzamarias D Spt3 and Mot1 cooperate in nucleosome remodeling independently of TBP recruitment EMBO J 2004, 23(9):1943-1948. 404319 15057269 10.1038/sj.emboj.7600199
22. Shen X Mizuguchi G Hamiche A Wu C et al A chromatin remodelling complex involved in transcription and DNA processing Nature 2000, 406(6795):541-544. 10.1038/35020123 10952318
23. Hughes TR Marton MJ Jones AR Roberts CJ Stoughton R Armour CD Bennett HA Coffey E Dai H He YD Functional discovery via a compendium of expression profiles Cell 2000, 102(1):109-126. 10.1016/S0092-8674(00)00015-5 10929718
24. Hu Z Killion PJ Iyer VR Genetic reconstruction of a functional transcriptional regulatory network Nat Genet 2007, 39(5):683-687. 10.1038/ng2012 17417638
25. Kimura H Cook PR Kinetics of core histones in living human cells: Little exchange of H3 and H4 and some rapid exchange of H2B J Cell Biol 2001, 153(7):1341-1353. 2150718 11425866 10.1083/jcb.153.7.1341
26. Holstege FC Jennings EG Wyrick JJ Lee TI Hengartner CJ Green MR Golub TR Lander ES Young RA Dissecting the regulatory circuitry of a eukaryotic genome Cell 1998, 95(5):717-728. 10.1016/S0092-8674(00)81641-4 9845373
27. Dion MF Kaplan T Kim M Buratowski S Friedman N Rando OJ Dynamics of replication-independent histone turnover in budding yeast Science 2007, 315(5817):1405-1408. 10.1126/science.1134053 17347438
28. Krebs JE Fry CJ Samuels ML Peterson CL Global role for chromatin remodeling enzymes in mitotic gene expression Cell 2000, 102(5):587-598. 10.1016/S0092-8674(00)00081-7 11007477
29. Syntichaki P Topalidou I Thireos G The Gcn5 bromodomain co-ordinates nucleosome remodelling Nature 2000, 404(6776):414-417. 10.1038/35006136 10746732
30. Recht J Osley MA Mutations in both the structured domain and N-terminus of histone H2B bypass the requirement for Swi-Snf in yeast Embo J 1999, 18(1):229-240. 1171117 9878065 10.1093/emboj/18.1.229
31. Breitkreutz BJ Stark C Reguly T Boucher L Breitkreutz A Livstone M Oughtred R Lackner DH Bahler J Wood V et al The BioGRID Interaction Database: 2008 update Nucleic Acids Res 2008, 36(Database):D637-640. 2238873 18000002
32. Martin AM Pouchnik DJ Walker JL Wyrick JJ Redundant roles for histone H3 N-terminal lysine residues in subtelomeric gene repression in Saccharomyces cerevisiae Genetics 2004, 167(3):1123-1132. 1470950 15280228 10.1534/genetics.104.026674
33. Hu Z Killion PJ Iyer VR Genetic reconstruction of a functional transcriptional regulatory network Nat Genet 2007, 39(5):683-687. 10.1038/ng2012 17417638
34. Lee W Tillo D Bray N Morse RH Davis RW Hughes TR Nislow C A high-resolution atlas of nucleosome occupancy in yeast Nat Genet 2007, 39(10):1235-1244. 10.1038/ng2117 17873876
35. Shivaswamy S Bhinge A Zhao Y Jones S Hirst M Iyer VR Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation PLoS Biol 2008, 6(3):e65. 2267817 18351804 10.1371/journal.pbio.0060065
36. Segal E Fondufe-Mittendorf Y Chen L Thastrom A Field Y Moore IK Wang JP Widom J A genomic code for nucleosome positioning Nature 2006, 442(7104):772-778. 2623244 16862119 10.1038/nature04979
37. Harbison CT Gordon DB Lee TI Rinaldi NJ Macisaac KD Danford TW Hannett NM Tagne JB Reynolds DB Yoo J et al Transcriptional regulatory code of a eukaryotic genome Nature 2004, 431(7004):99-104. 10.1038/nature02800 15343339
38. Pham H Ferrari R Cokus SJ Kurdistani SK Pellegrini M Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae Mol Syst Biol 2007, 3(153):18.
39. Yuan GC Ma P Zhong W Liu JS Statistical assessment of the global regulatory role of histone acetylation in Saccharomyces cerevisiae Genome Biol 2006, 7(8):R70. 1779595 16884527 10.1186/gb-2006-7-8-r70
40. Lee CK Shibata Y Rao B Strahl BD Lieb JD Evidence for nucleosome depletion at active regulatory regions genome-wide Nat Genet 2004, 36(8):900-905. 10.1038/ng1400 15247917
41. Basehoar AD Zanton SJ Pugh BF Identification and distinct regulation of yeast TATA box-containing genes Cell 2004, 116(5) 699-709. 10.1016/ S0092-8674(04)00205-3 15006352
42. Albert I Mavrich TN Tomsho LP Qi J Zanton SJ Schuster SC Pugh BF Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome Nature 2007, 446(7135):572-576. 10.1038/ nature05632 17392789
43. Liu CL Kaplan T Kim M Buratowski S Schreiber SL Friedman N Rando OJ Single-nucleosome mapping of histone modifications in S. cerevisiae PLoS Biol 2005, 3(10):e328. 1195719 16122352 10.1371/journal.pbio.0030328
44. Steinmetz EJ Warren CL Kuehner JN Panbehi B Ansari AZ Brow DA Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase Mol Cell 2006, 24(5):735-746. 10.1016/j.molcel.2006.10.023 17157256
45. Mellor J The dynamics of chromatin remodeling at promoters Mol Cell 2005, 19(2):147-157. 10.1016/j.molcel.2005.06.023 16039585
46. Saccharomyces Genome Database http://www.yeastgenome.org/
47. Stanford Microarray Database http://genome-www5.stanford.edu/