Transcriptional interaction-assisted identification of dynamic nucleosome positioning

BMC Bioinformatics

Volumn 10, Issue SUPPL. 1, 2009, Pages

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

^a SUN YAT SEN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR CONDITIONS; COMPUTATIONAL APPROACH; GENE EXPRESSION LEVELS; GENOMIC SEQUENCE; NUCLEOSOME POSITIONS; PREDICTION ACCURACY; REGULATORY PROTEIN; SEQUENCE INFORMATIONS;

COMPUTATIONAL METHODS; TRANSCRIPTION;

TRANSCRIPTION; BIOINFORMATICS;

DNA;

ARTICLE; BIOLOGY; GENETIC TRANSCRIPTION; GENETICS; GENOMICS; METHODOLOGY; NUCLEOSOME; NUCLEOTIDE SEQUENCE; REPRODUCIBILITY;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DNA; GENOMICS; NUCLEOSOMES; REPRODUCIBILITY OF RESULTS; TRANSCRIPTION, GENETIC;

EID: 60849112566     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S1-S31     Document Type: Conference Paper

References (49)

1. Kornberg RD Lorch Y Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome Cell 1999, 98:285-294. 10.1016/ S0092-8674(00)81958-3 10458604
2. Richmond TJ Davey CA The structure of DNA in the nucleosome core Nature 2003, 423:145-150. 10.1038/nature01595 12736678
3. Luger K Hansen JC Nucleosome and chromatin fiber dynamics Curr Opin Struc Biol 2005, 15:188-196. 10.1016/j.sbi.2005.03.006
4. Flaus A Hughes TO Mechanisms for ATP-dependent chromatin remodeling Curr Opin Genet Dev 2001, 11:148-154. 10.1016/S0959-437X(00)00172-6 11250137
5. Kouzarides T Chromatin modifications and their function Cell 2007, 128:693-705. 10.1016/j.cell.2007.02.005 17320507
6. Henikoff S Ahmad K Assembly of variant histones into chromatin Annu Rev Cell Dev Biol 2005, 21:133-153. 10.1146/annurev.cellbio.21.012704.133518 16212490
7. Yuan G Liu Y Dion MF Slack MD Wu LF Altschuler SJ Rando OJ Genome-scale identification of nucleosome positions in S. cerevisiae Science 2005, 309:626-630. 10.1126/science.1112178 15961632
8. 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, 39:1235-1244. 10.1038/ng2117 17873876
9. Whitehouse I Rando OJ Delrow J Tsukiyama T Chromatin remodeling at promoters suppresses antisense transcription Nature 2007, 450:1031-1035. 10.1038/nature06391 18075583
10. 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. doi:10.1371/ journal.pbio.0060065. 2267817 18351804 10.1371/journal.pbio.0060065
11. 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, 446:572-576. 10.1038/ nature05632 17392789
12. Ozsolak F Song JS Liu XS Fisher DE High-throughput mapping of the chromatin structure of human promoters Nat Biotechnol 2007, 25:244-248. 10.1038/nbt1279 17220878
13. Schones DE Cui K Cuddapah S Roh TY Barski A Wang Z Wei G Zhao K Dynamic regulation of nucleosome positioning in the human genome Cell 2008, 132:887-898. 10.1016/j.cell.2008.02.022 18329373
14. Barski A Cuddapah S Cui K Roh TY Schones DE Wang Z Wei G Chepelev L Zhao K High-resolution profiling of histone methylations in the human genome Cell 2007, 129:823-837. 10.1016/j.cell.2007.05.009 17512414
15. Widom J Role of DNA sequence in nucleosome stability and dynamics Q Rev Biophys 2001, 34:269-324. 11838235
16. Yuan GC Liu JS Genomic sequence is highly predictive of local nucleosome depletion PLoS Comput Biol 2008, 4(1):e13. doi:10.1371/ journal.pcbi.0040013. 2211532 18225943 10.1371/journal.pcbi.0040013
17. Ioshikhes IP Albert I Zanton SJ Pugh BF Nucleosome positions predicted through comparative genomics Nat Genet 2006, 38:1210-1215. 10.1038/ ng1878 16964265
18. Segel E Mittendorf YF Chen L Thastrom A Field Y A genomic code for nucleosome positioning Nature 2006, 442:772-778. 10.1038/nature04979 16862119 2623244
19. Pechham HE Thurman RE Fu Y Stamatoyannopoulos JA Noble WS Struhl K Weng Z Nucleosome positioning signals in genomic DNA Genome Res 2007, 17:1170-1177. 1933512 17620451 10.1101/gr.6101007
20. Whitehouse I Tsukiyama T Antagonistic forces that position nucleosomes in vivo Nat Struct Mol Biol 2006, 13:633-640. 10.1038/nsmb1111 16819518
21. Mellor J Dynamic nucleosomes and gene transcription Trends Genet 2006, 22:320-329. 10.1016/j.tig.2006.03.008 16631276
22. Berger SL The complex language of chromatin regulation during transcription Nature 2007, 447:407-412. 10.1038/nature05915 17522673
23. Mellor J The dynamics of chromatin remodeling at promoters Mol Cell 2005, 19:147-157. 10.1016/j.molcel.2005.06.023 16039585
24. Hogan GJ Lee CK Lieb JD Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters PLoS Genet 2006, 2(9):e158. DOI: 10.1371/ journal.pgen.0020158. 1570381 17002501 10.1371/journal.pgen.0020158
25. Narlikar L Gordan R Hartemink AJ A nucleosome-guided map of transcription factor binding sites in yeast PLoS Comput Biol 2007, 3(11):e215. doi:10.1371/journal.pcbi.0030215. 2065891 17997593 10.1371/ journal.pcbi.0030215
26. Sekinger EA Moqtaderi Z Struhl K Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast Mol Cell 2005, 18:735-748. 10.1016/ j.molcel.2005.05.003 15949447
27. Spellman PT Sherlock G Zhang MQ Iyer VR Anders K Eisen MB Brown PO Botstein D Futcher B Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization Mol Biol Cell 1998, 9:3273-3297. 25624 9843569
28. Santoro R Lucia FD Many players, one goal how chromatin states are inherited during cell division Biochem Cell Biol 2005, 83:332-343. 10.1139/o05-021 15959559
29. Gasch AP Spellman PT Kao CM Harel OC Eisen MB Storz G Botstein D Brown PO Genomic expression programs in the response of yeast cells to environmental changes Mol Biol Cell 2000, 11:4241-4257. 15070 11102521
30. Pokholok DK Harbison CT Levine S Cole M Hannett NM Lee TI Bell GW Walker K Rolfe PA Herbolsheimer E Zeitlinger J Lewitter F Gifford DK Young RA Genome-wide map of nucleosome acetylation and methylation in yeast Cell 2005, 122:517-527. 10.1016/j.cell.2005.06.026 16122420
31. Kamakaka RT Biggins S Histone variants: Deviants? Gene Dev 2005, 19:295-316. 10.1101/gad.1272805 15687254
32. Derisi JL Iyer VR Brown PO Exploring the metabolic and genetic control of gene expression on a genomic scale Science 1997, 278:680-686. 10.1126/ science.278.5338.680 9381177
33. Gasch AP Huang M Metzner S Botstein D Elledge SJ Brown PO Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p Mol Biol Cell 2001, 12:2987-3003. 60150 11598186
34. Chu S Derisi J Eisen M Mulholland J Botstein D Brown PO Herskowitz I The transcriptional program of sporulation in budding yeast Science 1998, 282:699-705. 10.1126/science.282.5389.699 9784122
35. Holstege FCP Jennings EG Wyrich JJ Lee TI Hengartner CJ Green MR Golub TR Lander ES Young RA Dissecting the regulatory circuitry of a eukaryotic genome Cell 1998, 95:717-728. 10.1016/S0092-8674(00)81641-4 9845373
36. 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 15247917
37. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Harris MA Hill DP Tarver LI Kasarskis A Lewis S Matese JC Richardson JE Ringwald M Rubin GM Sherlock G Gene Ontology tool for the unification of biology Nat Genet 2000, 25:25-29. 10.1038/75556 10802651
38. Liu X Lee CK Granek JA Clarke ND Lieb JD Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection Genome Res 2006, 16:1517-1528. 1665635 17053089 10.1101/gr.5655606
39. Tanay A Extensive low-affinity transcriptional interactions in the yeast genome Genome Res 2006, 16:962-972. 1524868 16809671 10.1101/gr.5113606
40. Dodd IB Micheelsen MA Sneppen K Thon G Theoretical analysis of epigenetic cell memory by nucleosome modification Cell 2007, 129:813-822. 10.1016/j.cell.2007.02.053 17512413
41. Sneppen K Micheelsen MA Dodd IB Ultrasensitive gene regulation by positive feedback loops in nucleosome modification Mol Syst Biol 2008, 15 April. doi:10.1038/msb.2008.21. 2387233 18414483
42. The Saccharomyces Genome Database http://www.yeastgenome.org
43. Harbison CT Gordon DB Lee TI Rinaldi NJ Macisaac KD Danford TW Hannett NM Tagne J Reynolds DB Yoo J Jennings EG Zeitlinger J Pokholok DK Kellis M Rolfe PA Takusagawa KT Lander ES Gifford DK Fraenkel E Young RA Transcriptional regulatory code of a eukaryotic genome Nature 2004, 431:99-104. 10.1038/nature02800 15343339
44. Simon I Barnett J Hannett N Harbison CT Rinaldi NJ Volkert TL Wyrich JJ Zeitlinger J Gifford DK Jaakkola TS Young RA Serial regulation of transcriptional regulators in the yeast cell cycle Cell 2001, 106:697-708. 10.1016/S0092-8674(01)00494-9 11572776
45. Tsai HK Chou MY Shih CH Huang GTW Chang TH Li WH MYBS: A comprehensive web server for mining transcription factor binding sites in yeast Nucleic Acids Res 2007, 35:W221-W226. 1933147 17537814 10.1093/nar/gkm379
46. Ghaemmaghami S Huh WK Bower K Howson RW Belle A Dephoure N Oshea EK Weissman JS Global analysis of protein expression in yeast Nature 2003, 425:737-741. 10.1038/nature02046 14562106
47. Lu P Vogel C Wang R Yao X Marcotte EM Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation Nat Biotechnol 2007, 25:117-124. 10.1038/ nbt1270 17187058
48. Luscombe NM Babu MM Yu H Snyder M Teichmann SA Gerstein M Genomic analysis of regulatory network dynamics reveals large topological changes Nature 2004, 431:308-312. 10.1038/nature02782 15372033
49. Jansen R Greenbaum D Gerstein M Relating whole-genome expression data with protein-protein interactions Genome Res 2002, 12:37-46. 155252 11779829 10.1101/gr.205602