Characterizing nucleosome dynamics from genomic and epigenetic information using rule induction learning

BMC Genomics

Volumn 10, Issue SUPPL. 3, 2009, Pages

  Le, Ngoc T ^a,b   Ho, Tu B ^a,c   Tran, Dang H ^a,b  

^a JAPAN ADVANCED INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^b HANOI NATIONAL UNIVERSITY OF EDUCATION   (Viet Nam)

^c GRADUATE UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Viet Nam)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL DNA; HISTONE;

ARTICLE; CHROMOSOME 3; DNA SEQUENCE; EPIGENETICS; GENE ACTIVATION; GENE INDUCTION; GENE REPRESSION; GENOMICS; NONHUMAN; NUCLEOSOME; PROMOTER REGION; PROTEIN PROCESSING; SACCHAROMYCES CEREVISIAE; CHEMISTRY; GENETIC EPIGENESIS; GENETICS; GENOME; METABOLISM; METHODOLOGY; NUCLEOTIDE SEQUENCE;

EUKARYOTA;

BIOLOGICAL PROCESS; CHROMATIN REMODELLING; COMPACT STRUCTURES; DNA MOTIF; DNA REPAIR; EUKARYOTIC GENOME; HISTONE MODIFICATION; HISTONE PROTEINS; NUCLEOSOMES; POST-TRANSLATIONAL MODIFICATIONS; PROMOTER REGION; REGULATORY ELEMENTS; REPEATING UNIT; RULE INDUCTION; S.CEREVISIAE; TRANSCRIPTIONAL ACTIVITY;

DNA; DYNAMICS; GENES; MACHINERY; PROTEINS; STABILITY;

BIOINFORMATICS;

BASE SEQUENCE; EPIGENESIS, GENETIC; GENOME; GENOMICS; HISTONES; NUCLEOSOMES; PROTEIN PROCESSING, POST-TRANSLATIONAL; SACCHAROMYCES CEREVISIAE;

EID: 71549146868     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-S3-S27     Document Type: Article

References (36)

1. Luger K, Mader AW, Richmond AK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 1997, 389:251-260. 10.1038/38444, 9305837.
2. Kornberg RD, Thomas JO. Chromatin structure; oligomers of the histones. Science 1974, 184(139):865-868. 10.1126/science.184.4139.865, 4825888.
3. Groth A, Rocha W, Verreault A, Almouzni G. Chromatin Challenges during DNA Replication and Repair. Cell 2007, 128(4):721-733. 10.1016/j.cell.2007.01.030, 17320509.
4. Li B, Carey M, Workman JL. The Role of Chromatin during Transcription. Cell 2007, 128(4):707-719. 10.1016/j.cell.2007.01.015, 17320508.
5. Corpet A, Almouzni G. Making copies of chromatin: the challenge of nucleosomal organization and epigenetic information. Trends in Cell Biology 2008, 19:29-41. 10.1016/j.tcb.2008.10.002, 19027300.
6. Probst AV, Dunleavy E, Almouzni G. Epigenetic inheritance during the cell cycle. Nature Reviews Molecular Cell Biology 2009, 10:192-206. 10.1038/nrm2640, 19234478.
7. Lee CK, Shibata Y, Rao B, Strah BD, Lieb JD. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nature Genetics 2004, 36:900-905. 10.1038/ng1400, 15247917.
8. Henikoff S. Nucleosomes at active promoters: unforgettable loss. Cancer cell 2007, 12(5):407-409. 10.1016/j.ccr.2007.10.024, 17996642.
9. Henikoff S. Nucleosome destabilization in the epigenetic regulation of gene expression. Nature Reviews Genetics 2008, 9:15-26. 10.1038/nrg2206, 18059368.
10. Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, Moore IK, Wang JPZ, Widom J. A genomic code for nucleosome positioning. Nature 2006, 442(7104):772-778. 10.1038/nature04979, 2623244, 16862119.
11. Reinke H, Horz W. Histones Are First Hyperacetylated and Then Lose Contact with the Activated PHO5 Promoter. Molecular Cell 2003, 11(6):1599-1607. 10.1016/S1097-2765(03)00186-2, 12820972.
12. Zhao J, Diaz JH, Gross DS. Domain-Wide Displacement of Histones by Activated Heat Shock Factor Occurs Independently of Swi/Snf and Is Not Correlated with RNA Polymerase II Density. Molecular and Cellular Biology 2005, 25(20):8985-8999. 10.1128/MCB.25.20.8985-8999.2005, 1265789, 16199876.
13. Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ. Genome-Scale Identification of Nucleosome Positions in S. cerevisiae. Science 2005, 309(5734):626-630. 10.1126/science.1112178, 15961632.
14. Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C. A high-resolution atlas of nucleosome occupancy in yeast. Nature Genetics 2007, 39(10):1235-1244. 10.1038/ng2117, 17873876.
15. Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, Zanton SJ, Tomsho LP, Qi J, Glaser RL, Schuster SC, Gilmour DS, IstvanAlbert, Pugh BF. Nucleosome organization in the Drosophila genome. Nature 2008, 453:358-362. 10.1038/nature06929, 2735122, 18408708.
16. 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(4):517-527. 10.1016/j.cell.2005.06.026, 16122420.
17. Liu CL, Kaplan T, Kim M, Buratowski S, Schreiber SL, Friedman N, Rando OJ. Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biology 2005, 3(10). 10.1371/journal.pbio.0030328, 1195719,1195719, 16122352.
18. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-Resolution Profiling of Histone Methylations in the Human Genome. Cell 2007, 129(4):823-837. 10.1016/j.cell.2007.05.009, 17512414.
19. Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, Struhl K, Weng Z. Nucleosome positioning signals in genomic DNA. Genome Research 2007, 17(8):1170-1177. 10.1101/gr.6101007, 1933512, 17620451.
20. Zhang Y, Shin H, Song JS, Lei Y, Liu XS. Identifying Positioned Nucleosomes with Epigenetic Marks in Human from ChIP-Seq. BMC Genomics 2008, 9:537. 2267712, 18186939, 10.1186/1471-2164-9-537.
21. Rippe K, Schrader A, Riede P, Strohner R, Lehmann E, Langst G. DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes. Proceedings of the National Academy of Sciences of the United States of America 2007, 104(40):15635-15640. 10.1073/pnas.0702430104, 2000439, 17893337.
22. Schnitzler GR. Control of Nucleosome Positions by DNA Sequence and Remodeling Machines. Cell Biochemistry and Biophysics 2008, 51(2-3):67-80. 10.1007/s12013-008-9015-6, 18543113.
23. Widlund HR, Vitolo M, Thiriet C, Hayes JJ. DNA sequence-dependent contributions of core histone tails to nucleosome stability: differential effects of acetylation and proteolytic tail removal. Biochemistry 2000, 39(13):3835-3841. 10.1021/bi991957l, 10736184.
24. Yang Z, Zheng C, Hayes JJ. The core histone tail domains contribute to sequence-dependent nucleosome positioning. Journal of Biological Chemistry 2007, 282(11):7930-7938. 10.1074/jbc.M610584200, 17234628.
25. Dai Z, Dai X, Xiang Q, Feng J, Deng Y, Wang J, He C. Transcriptional interaction-assisted identification of dynamic nucleosome positioning. BMC Bioinformatics 2009, 10(Suppl l):S31. 10.1186/1471-2105-10-S1-S31, 2648733, 19208132.
26. Lavrac N, Kavsek B, Flach P, Todorovski L. Subgroup discovery with CN2-SD. Journal of Machine Learning Research 2004, 5:153-188.
27. Wang G, Zhang W. A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements. Genome Biology 2006, 7(6). 1779545, 16787547.
28. Das MK, Dai HK. A survey of DNA motif finding algorithms. BMC Bioinformatics 2007, 8(Suppl 7):S21. 10.1186/1471-2105-8-S7-S21, 2099490, 18047721.
29. Kurdistani SK, Tavazoie S, Grunstein M. Mapping global histone acetylation patterns to gene expression. Cell 2004, 117(6):721-733. 10.1016/j.cell.2004.05.023, 15186774.
30. Hebbes TR, Thorne AW, Crane-Robinson C. A direct link between core histone acetylation and transcriptionally active chromatin. The EMBO Journal 1988, 7(5):1395-1402. 458389, 3409869.
31. Wang A, Kurdistani SK, Grunstein M. Requirement of Hos2 histone deacetylase for gene activity in yeast. Science 2002, 298(5597):1412-1414. 10.1126/science.1077790, 12434058.
32. de Nadal E, Zapater M, Alepuz PM, Sumoy L, Mas G, Posas F. The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive genes. Nature 2004, 427(6972):370-374. 10.1038/nature02258, 14737171.
33. Jiang C, Pugh BF. Nucleosome positioning and gene regulation: advances through genomics. Nature Reviews Genetics 2009, 10:161-172. 10.1038/nrg2522, 19204718.
34. Pavlidis P, Wapinski I, Noble WS. Support vector machine classification on the web. Bioinformatics 2004, 20:586-587. 10.1093/bioinformatics/btg461, 14990457.
35. Clark P, Nibblet T. The CN2 induction algorithm. Machine Learning 1989, 3:261-283.
36. Pham TH, Clemente JC, Satou K, Ho TB. Computational discovery of transcriptional regulatory rules. Bioinformatics 2005, 21:ii101-ii107. 10.1093/bioinformatics/bti1117, 16204087.