Quantitatively assessing the effects of regulatory factors on nucleosome dynamics by multiple kernel learning
详细信息 查看全文
- 作者：Bich Hai Ho (1) haihb@jaist.ac.jp
Ngoc Tu Le (1) ngoctule@jaist.ac.jp
Tu Bao Ho (2) bao@jaist.ac.jp - 关键词：Nucleosome dynamics – ; Post ; translational histone modification – ; Multiple kernel learning – ; Genomic sequence
- 刊名：Journal of Ambient Intelligence and Humanized Computing
- 出版年：2012
- 出版时间：December 2012
- 年：2012
- 卷：3
- 期：4
- 页码：315-323
- 全文大小：373.1 KB
- 参考文献：1. Anderson J, Lowary P, Widom J (2001) Effects of histone acetylation on the equilibrium accessibility of nucleosomal DNA target sites. J Mol Biol 307:977–985
2. Bach F, Lanckriet G, Jordan M (2004) Multiple kernel learning, conic duality, and the smo algorithm. In: Proceedings of the 21st international conference on machine learning (ICML)
3. Breiman L (2001) Randome forests. Mach Learn 45(1):5–32
4. Bryan K, Brennan L, Cunningham P (2001) MetaFIND: A feature analysis tool for metabolomics data. BMC Bioinform 9(1):470
5. Gehler PV, Nowozin S (2008) Infinite kernel learning. Tech. report. Max Planck Institute for Biological Cybernetics
6. Gupta S, Dennis J, Thurman R, Kingston R, Stamatoyannopoulos J, Noble W (2008) Predicting human nucleosome occupancy from primary sequence. PLoS Comput Biol 4(8):e1000134
7. Henikoff S (2008) Nucleosome destabilization in the epigenetic regulation of gene expression. Nat Rev Genet 9:15–26
8. Hou Y, Zhou X, Liu J, Yuan J, Cheng H, Zhou R (2010) Nuclear factor-y (NF-Y) regulates transcription of mouse dmrt7 gene by binding to tandem CCAAT boxes in its proximal promoter. Int J Biol Sci 6(7):655–664
9. Jansen A, Verstrepen K (2011) Nucleosome positioning in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 75(2):310–20
10. Kaplan N, Moore I, Fondufe-Mittendorf Y, Gossett A, Tillo D, Field Y, LeProust E, Hughes T, JD JL, Widom J, Segal E (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458(7236):362–366
11. Kurdistani S, Grunstein M (2003) Histone acetylation and deacetylation in yeast. Nat Rev Mol Cell Biol 4:276–284
12. Lanckriet G, Deng M, Cristianini N, Jordan M, Noble W (2004) Kernel-based data fusion and its application to protein function prediction in yeast. In: Proceedings of the Pacific symposium on biocomputing, pp 300–311
13. Le N, Ho T, Tran D (2009) Characterizing nucleosome dynamics from genomic and epigenetic information using rule inductiong learning. BMC Genomics 10(3):S27
14. LeRoy G, BRickards, Flint S (2008) The double bromodomain proteins brd2 and brd3 couple histone acetylation to transcription. BMC Bioinform 30(1):51–60
15. Li B, Carey M, Workman J (2007) The role of chromatin during transcription. Cell 128(4):707–719
16. Liu C, Kaplan T, Kim M, Buratowski S, Schreiber S, Friedman N, Rando O (2005) Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol 3(10):1753–1769
17. Luger K, M盲der A, Richmond R, Sargent D, Richmond T (1997) Crystal structure of the nucleosome core particle at 2.8 a resolution. Nature 389:251–260
18. Oliver S, Denu J (2011) Dynamic interplay between histone h3 modifications and protein interpreters: emerging evidence for a ”histone language”. Chembiochem 12(2):299–307
19. 脰z枚g眉r Aky眉z S, Weber G (2008) Learning with infinitely many kernels via semi-infinite programming. In: Proceedings of continuous optimization and knowledge based technologies, 20th EURO mini conference, pp 342–348
20. 脰z枚g眉r Aky眉z S, Weber G (2009) Modelling of kernel machines by infinite and semi-infinite programming. In: Proceedings of the second global conference on power control and optimization, pp 306–313
21. 脰z枚g眉r Aky眉z S, Weber G (2010) On numerical optimization theory of infinite kernel learning. J Global Optim 48(2):215–239
22. Peckham H, Thurman R, Y YF, Stamatoyannopoulos J, Noble W, Struhl K, Weng Z (2007) Nucleosome positioning signals in genomic DNA. Genome Res 17(8):1170–1177
23. Polach K, Lowary P, Widom J (2000) Effects of core histone tail domains on the equilibrium constants for dynamic DNA site accessibility in nucleosomes. J Mol Biol 298:211–223
24. Prost A, Dunleavy E, Almouzni G (2009) Epigenetic inheritance during the cell cycle. Nat Rev Mol Cell Biol 10:192–206
25. Ratsch G, Sonnenburg S, Schafer C (2006) Learning interpretable SVMs for biological sequence classification. BMC Bioinform 7(1):S9
26. Reif D, Motsinger A, McKinney B, Crowe J, Moore J (2006) Feature selection using a random forests classifier for the integrated analysis of multiple data types. In: 2006 IEEE symposium on computational intelligence and bioinformatics and computational biology, CIBCB ’06, pp 1–8
27. Rippe K, Schrader A, Riede P, Strohner R, Lehmann E, L盲ngst G (2007) DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodelling complexes. Proc Natl Acad Sci USA 104(40):15635–15640
28. Schnitzler G (2008) Control of nucleosome positions by DNA sequence and remodelling machines. Cell Biochem Biophys 51(2–3):67–80
29. Schwartz S, Meshorer E, Ast G (2009) Chromatin organization marks exon-intron structure. Nat Struct Mol Biol 16(9):990–995
30. Segal E, Widom J (2009) What controls nucleosome positions? Trends Genet 25(8):335–43
31. Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, Moore I, Wang J, Widom J (2006) A genomic code for nucleosome positioning. Nature 442(7104):772–778
32. Sonnenburg S, Ratsch G, Schafer C, Scholkopf B (2006) Large scale multiple kernel learning. J Mach Learn Res 7:1531–1565
33. Tanaka Y, Yoshimura I, Nakai K (2010) Positional variations among heterogeneous nucleosome maps give dynamical information on chromatin. Chromosoma 119:391–404
34. Tillo D, Hughes T (2009) G+C content dominates intrinsic nucleosome occupancy. BMC Bioinform 10:442
35. Tue N, Yoshioka Y, Yamaguchi M (2011) NF-Y transcriptionally regulates the drosophila p53 gene. Genes 473(1):1–7
36. Wan J, Lin J, Zack D, Qian J (2009) Regulating periodicity of nucleosome organization and gene regulation. Bioinformatics 25(14):1782–1788
37. Waterborg J (2002) Dynamics of histone acetylation in vivo. A function for acetylation turnover? Biochem Cell Biol 8:363–378
38. Widlund H, Vitolo J, Thiriet C, Hayes J (2000) DNA sequence-dependent contributions of core histone tails to nucleosome stability: differential effects of acetylation and proteolytic tail removal. Biochemistry 39:3835–3641
39. Windom J (2001) Role of dna sequence in nucleosome stability and dynamics. Q Rev Biophys 34(3):269–324
40. Wir茅n M, Silverstein R, Sinha I, Walfridsson J, Lee H, Laurenson P, Pillus L, Robyr D, Grunstein M, Ekwall K (2005) Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast. EMBO J 24(16):2906–2918
41. Yang Z, Zheng C, Hayes J (2007) The core histone tail domains contribute to sequence-dependent nucleosome positioning. J Biol Chem 282(11):7930–8
42. Yuan G, Liu Y, Dion M, Slack M, LF LW, Altschuler S, Rando O (2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309:626–630
43. Zhao J, Herrera-Diaz J, Gross D (2005) Domain-wide displacement of histones by activated heat shock factor occurs independently of swi/snf and is not correlated with RNA polymerase II density. Mol Cell Biol 25(20):8985–8999 - 作者单位：1. School of Knowledge Science, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan2. John von Neumann Institute, Vietnam National University, Ho Chi Minh, Vietnam
- ISSN：1868-5145
文摘
Nucleosome, a nucleoprotein structure formed by coiling 147 bp of DNA around an octamer of histone proteins, is the fundamental repeating unit of eukaryotic chromatin. By regulating the access of biological machineries to underlying cis-regulatory elements, its mobility has been implicated in many important cellular processes. Although it has been known that various factors, such as DNA sequences, histone modifications, etc., cooperatively affect nucleosome mobility, the contribution of each factor in the common impact remains unclear. We propose, in this work, a novel computational approach based on multiple kernel learning for quantitatively assessing the effects of two important factors, i.e., genomic sequence and post-translational histone modifications (PTMs), on nucleosome dynamics. Our result on Saccharomyces cerevisiae shows that, epigenetic feature, such as histone modifications, plays more important role than genomic sequence in regulating nucleosome dynamics. Based on that, we carried further analysis on each PTM to reveal their combinatory effects on nucleosome dynamics and found out that some pairs of PTMs such as H3K9Ac–H4H14Ac, H4K5Ac–H4K12Ac and H4K5Ac–H3K14Ac might co-operate in altering nucleosome stability in gene regulation.