Modelling epigenetic regulation of gene expression in 12 human cell types reveals combinatorial patterns of cell-type-specific genes

IET Systems Biology

Volumn 8, Issue 3, 2014, Pages 104-115

  Lu, Yiming ^a   Qu, Wubin ^a   Min, Bo ^a   Liu, Zheyan ^a   Chen, Changsheng ^b   Zhang, Chenggang ^a  

^a BEIJING INSTITUTE OF RADIATION MEDICINE   (China)

^b FOURTH MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CELLS; CYTOLOGY; GENE EXPRESSION REGULATION; GENES;

CELL TYPES; DYNAMIC CHANGES; EPIGENETIC REGULATION; HISTONE MODIFICATION; HUMAN CELLS; MULTICELLULAR ORGANISMS; QUANTITATIVE MODELS; REGULATORY RELATIONSHIPS;

GENE EXPRESSION;

HISTONE;

ALGORITHM; ARTICLE; BIOLOGY; CELL LINE; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; HUMAN; HUMAN GENOME; METABOLISM; METHODOLOGY; PROMOTER REGION; SEQUENCE ANALYSIS; TUMOR CELL LINE;

ALGORITHMS; CELL LINE; CELL LINE, TUMOR; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; EPIGENESIS, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOME, HUMAN; HISTONES; HUMANS; PROMOTER REGIONS, GENETIC; SEQUENCE ANALYSIS, RNA;

EID: 84906925950     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb.2013.0042     Document Type: Article

References (49)

1. Maston, G.A., Evans, S.K., Green, M.R.: 'Transcriptional regulatory elements in the human genome', Annu. Rev. Genomics Hum. Genet., 2006, 7, pp. 29-59
2. Bernstein, B.E., Meissner, A., Lander, E.S.: 'The mammalian epigenome', Cell, 2007, 128, pp. 669-681
3. Kouzarides, T.: 'Chromatin modifications and their function', Cell, 2007, 128, pp. 693-705
4. Surani, M.A., Hayashi, K., Hajkova, P.: 'Genetic and epigenetic regulators of pluripotency', Cell, 2007, 128, pp. 747-762
5. Li, B., Carey, M., Workman, J.L.: 'The role of chromatin during transcription', Cell, 2007, 128, pp. 707-719
6. Bannister, A.J., Kouzarides, T.: 'Regulation of chromatin by histone modifications', Cell Res., 2011, 21, pp. 381-395
7. Roh, T.Y., Cuddapah, S., Cui, K., Zhao, K.: 'The genomic landscape of histone modifications in human T cells', Proc. Natl. Acad. Sci., 2006, 103, pp. 15782-15787
8. Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., et al.: 'High-resolution profiling of histone methylations in the human genome', Cell, 2007, 129, pp. 823-837
9. Wang, Z., Zang, C., Rosenfeld, J.A., Schones, D.E., Barski, A., et al.: 'Combinatorial patterns of histone acetylations and methylations in the human genome', Nat. Genet., 2008, 40, pp. 897-903
10. Koch, C.M., Andrews, R.M., Flicek, P., Dillon, S.C., Karaoz, U., et al.: 'The landscape of histone modifications across 1% of the human genome in five human cell lines', Genome Res., 2007, 17, pp. 691-707
11. Ucar, D., Hu, Q., Tan, K.: 'Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering', Nucleic Acids Res., 2011, 39, pp. 4063-4075
12. Ernst, J., Kellis, M.: 'Discovery and characterization of chromatin states for systematic annotation of the human genome', Nat. Biotechnol., 2010, 28, pp. 817-825
13. Karlic, R., Chung, H.R., Lasserre, J., Vlahovicek, K., Vingron, M.: 'Histone modification levels are predictive for gene expression', Proc. Natl. Acad. Sci., 2010, 107, pp. 2926-2931
14. Young, M.D., Willson, T.A., Wakefield, M.J., Trounson, E., Hilton, D. J., et al.: 'ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity', Nucleic Acids Res., 2011, 39, pp. 7415-7427
15. Zhang, Z., Zhang, M.Q.: 'Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes', BMC Bioinfor., 2011, 12, p. 155
16. Cheng, C., Gerstein, M.: 'Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells', Nucleic Acids Res., 2012, 40, pp. 553-568
17. Bernstein, B.E., Mikkelsen, T.S., Xie, X., Kamal, M., Huebert, D.J., et al.: 'A bivalent chromatin structure marks key developmental genes in embryonic stem cells', Cell, 2006, 125, pp. 315-326
18. Mikkelsen, T.S., Ku, M., Jaffe, D.B., Issac, B., Lieberman, E., et al.: 'Genome-wide maps of chromatin state in pluripotent and lineage-committed cells', Nature, 2007, 448, pp. 553-560
19. Heintzman, N.D., Hon, G.C., Hawkins, R.D., Kheradpour, P., Stark, A., et al.: 'Histone modifications at human enhancers reflect global cell-type-specific gene expression', Nature, 2009, 459, pp. 108-112
20. Ernst, J., Kheradpour, P., Mikkelsen, T.S., Shoresh, N., Ward, L.D., et al.: 'Mapping and analysis of chromatin state dynamics in nine human cell types', Nature, 2011, 473, pp. 43-49
21. Choi, J.K., Kim, Y.J.: 'Epigenetic regulation and the variability of gene expression', Nat. Genet., 2008, 40, pp. 141-147
22. Ha, M., Ng, D.W., Li, W.H., Chen, Z.J.: 'Coordinated histone modifications are associated with gene expression variation within and between species', Genome Res., 2011, 21, pp. 590-598
23. 'A user's guide to the encyclopedia of DNA elements (ENCODE)', PLoS Biol., 2011, 9, p. e1001046
24. Bernstein, B.E., Stamatoyannopoulos, J.A., Costello, J.F., Ren, B., Milosavljevic, A., et al.: 'The NIH Roadmap Epigenomics Mapping Consortium', Nat. Biotechnol., 2010, 28, pp. 1045-1048
25. Chepelev, I., Wei, G., Tang, Q., Zhao, K.: 'Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq', Nucleic Acids Res., 2009, 37, p. e106
26. Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., et al.: 'Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks', Nat. Protocols, 2012, 7, pp. 562-578
27. Fujita, P.A., Rhead, B., Zweig, A.S., Hinrichs, A.S., Karolchik, D., et al.: 'The UCSC genome browser database: update 2011', Nucleic Acids Res., 2011, 39, pp. D876-D882
28. Trapnell, C., Pachter, L., Salzberg, S.L.: 'TopHat: discovering splice junctions with RNA-Seq', Bioinformatics, 2009, 25, pp. 1105-1111
29. Roberts, A., Pimentel, H., Trapnell, C., Pachter, L.: 'Identification of novel transcripts in annotated genomes using RNA-Seq', Bioinformatics, 2011, 27, pp. 2325-2329
30. Saxonov, S., Berg, P., Brutlag, D.L.: 'A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters', Proc. Natl. Acad. Sci., 2006, 103, pp. 1412-1417
31. Roy, S., Ernst, J., Kharchenko, P.V., Kheradpour, P., Negre, N., et al.: 'Identification of functional elements and regulatory circuits by Drosophila modENCODE', Science, 2010, 330, pp. 1787-1797
32. Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., et al.: 'Model-based analysis of ChIP-Seq (MACS)', Genome Biol., 2008, 9, p. R137
33. Schug, J., Schuller, W.P., Kappen, C., Salbaum, J.M., Bucan, M., et al.: 'Promoter features related to tissue specificity as measured by Shannon entropy', Genome Biol., 2005, 6, p. R33
34. Tibshirani, R.: 'Regression shrinkage and selection via the lasso', J. R. Stat. Soc. B, Methodol., 1996, 58, pp. 267-288
35. Lu, Y., Zhou, Y., Qu, W., Deng, M., Zhang, C.: 'A Lasso regression model for the construction of microRNA-target regulatory networks', Bioinformatics, 2011, 27, pp. 2406-2413
36. Ihaka, R., Gentleman, R.: 'R: a language for data analysis and graphics', J. Comput. Graph. Stat., 1996, 5, pp. 299-314
37. Efron, B., Hastie, T., Johnstone, I., Tibshirani, R.: 'Least angle regression', Ann. Stat., 2004, 32, pp. 407-499
38. Farrar, D.E., Glauber, R.R.: 'Multicollinearity in regression analysis: the problem revisited', Rev. Econ. Stat., 1967, 49, pp. 92-107
39. Efron, B., Tibshirani, R.: 'An introduction to the bootstrap' (Chapman & Hall/CRC, 1993)
40. Ouyang, Z., Zhou, Q., Wong, W.H.: 'ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells', Proc. Natl. Acad. Sci., 2009, 106, pp. 21521-21526
41. Rousseeuw, P.J.: 'Silhouettes: a graphical aid to the interpretation and validation of cluster analysis', J. Comput. Appl. Math., 1987, 20, pp. 53-65
42. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., et al.: 'Gene ontology: tool for the unification of biology', Gene Ontology Consortium', Nat. Genet., 2000, 25, pp. 25-29
43. Maere, S., Heymans, K., Kuiper, M.: 'BiNGO: a cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks', Bioinformatics, 2005, 21, pp. 3448-3449
44. Loh, Y.H., Wu, Q., Chew, J.L., Vega, V.B., Zhang, W., et al.: 'The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells', Nat. Genet., 2006, 38, pp. 431-440
45. Boyer, L.A., Lee, T.I., Cole, M.F., Johnstone, S.E., Levine, S.S., et al.: 'Core transcriptional regulatory circuitry in human embryonic stem cells', Cell, 2005, 122, pp. 947-956
46. Reik, W.: 'Stability and flexibility of epigenetic gene regulation in mammalian development', Nature, 2007, 447, pp. 425-432
47. Yu, H., Zhu, S.S., Zhou, B., Xue, H.L., Han, J.D.J.: 'Inferring causal relationships among different histone modifications and gene expression (vol, pg 1314, 2008)', Genome Res., 2008, 18, pp. 1544-1544
48. Maruyama, R., Choudhury, S., Kowalczyk, A., Bessarabova, M., Beresford-Smith, B., et al.: 'Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium', PLoS Genet., 2011, 7, p. e1001369
49. Berger, S.L.: 'The complex language of chromatin regulation during transcription', Nature, 2007, 447, pp. 407-412