Discovery of cell-type specific regulatory elements in the human genome using differential chromatin modification analysis

Nucleic Acids Research

Volumn 41, Issue 20, 2013, Pages 9230-9242

  Chen, Chen ^a   Zhang, Shihua ^a   Zhang, Xiang Sun ^a  

^a CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGICAL ACTIVITY; CELL SPECIFICITY; CELL TYPE; CELL TYPE SPECIFIC REGULATORY ELEMENT; CHROMATIN; CONTROLLED STUDY; DATA ANALYSIS; DIFFERENTIAL CHROMATIN MODIFICATION ANALYSIS; GENE LOCATION; GENETIC CODE; GENOME ANALYSIS; HUMAN; HUMAN CELL; HUMAN GENOME; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROCESS DEVELOPMENT; REGULATORY SEQUENCE;

BINDING SITES; CHROMATIN; E1A-ASSOCIATED P300 PROTEIN; EPIGENESIS, GENETIC; EPIGENOMICS; GENOME, HUMAN; HISTONES; HUMANS; TRANSCRIPTION, GENETIC;

EID: 84890030725     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt712     Document Type: Article

References (52)

1. Maniatis, T., Goodbourn, S. and Fischer, J.A. (1987) Regulation of inducible and tissue-specific gene expression. Science, 236, 1237-1245.
2. Dong, X., Greven, M.C., Kundaje, A., Djebali, S., Brown, J.B., Cheng, C., Gingeras, T.R., Gerstein, M., Guigo, R., Birney, E. et al. (2012) Modeling gene expression using chromatin features in various cellular contexts. Genome Biol., 13, R53.
3. Karlic, R., Chung, H.R., Lasserre, J., Vlahovicek, K. and Vingron, M. (2010) Histone modification levels are predictive for gene expression. Proc. Natl Acad. Sci. USA, 107, 2926-2931.
4. Maunakea, A.K., Nagarajan, R.P., Bilenky, M., Ballinger, T.J., D'Souza, C., Fouse, S.D., Johnson, B.E., Hong, C., Nielsen, C., Zhao, Y. et al. (2010) Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature, 466, 253-257.
5. Crick, F. (1970) Central dogma of molecular biology. Nature, 227, 561-563.
6. Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I. and Zhao, K. (2007) High-resolution profiling of histone methylations in the human genome. Cell, 129, 823-837.
7. Azuara, V., Perry, P., Sauer, S., Spivakov, M., Jorgensen, H.F., John, R.M., Gouti, M., Casanova, M., Warnes, G., Merkenschlager, M. et al. (2006) Chromatin signatures of pluripotent cell lines. Nat. Cell Biol., 8, 532-538.
8. Bernstein, B.E., Mikkelsen, T.S., Xie, X., Kamal, M., Huebert, D.J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K. et al. (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell, 125, 315-326.
9. Cheng, C., Yan, K.K., Yip, K.Y., Rozowsky, J., Alexander, R., Shou, C. and Gerstein, M. (2011) A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets. Genome Biol., 12, R15.
10. Heintzman, N.D., Stuart, R.K., Hon, G., Fu, Y., Ching, C.W., Hawkins, R.D., Barrera, L.O., Van Calcar, S., Qu, C., Ching, K.A. et al. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet., 39, 311-318.
11. Ye, T., Krebs, A.R., Choukrallah, M.A., Keime, C., Plewniak, F., Davidson, I. and Tora, L. (2011) seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res., 39, e35.
12. Liu, T., Ortiz, J.A., Taing, L., Meyer, C.A., Lee, B., Zhang, Y., Shin, H., Wong, S.S., Ma, J., Lei, Y. et al. (2011) Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol., 12, R83.
13. Hon, G., Ren, B. and Wang, W. (2008) ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput. Biol., 4, e1000201.
14. Jaschek, R. and Tanay, A. (2009) Spatial clustering of multivariate genomic and epigenomic information. Res. Comput. Mol. Biol., 5541, 170-183.
15. Ernst, J. and Kellis, M. (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat. Biotechnol., 28, 817-825.
16. Hoffman, M.M., Buske, O.J., Wang, J., Weng, Z., Bilmes, J.A. and Noble, W.S. (2012) Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat. Methods, 9, 473-476.
17. Ucar, D., Hu, Q. and Tan, K. (2011) Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering. Nucleic Acids Res., 39, 4063-4075.
18. Teng, L. and Tan, K. (2012) Finding combinatorial histone code by semi-supervised biclustering. BMC Genomics, 13, 301.
19. Ernst, J., Kheradpour, P., Mikkelsen, T.S., Shoresh, N., Ward, L.D., Epstein, C.B., Zhang, X., Wang, L., Issner, R., Coyne, M. et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature, 473, 43-49.
20. Rozowsky, J., Euskirchen, G., Auerbach, R.K., Zhang, Z.D., Gibson, T., Bjornson, R., Carriero, N., Snyder, M. and Gerstein, M.B. (2009) PeakSeq enables systematic scoring of ChIPseq experiments relative to controls. Nat. Biotechnol., 27, 66-75.
21. Bolstad, B.M., Irizarry, R.A., Astrand, M. and Speed, T.P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193.
22. Klevecz, R.R. and Murray, D.B. (2001) Genome wide oscillations in expression. Wavelet analysis of time series data from yeast expression arrays uncovers the dynamic architecture of phenotype. Mol. Biol. Rep., 28, 73-82.
23. Thurman, R.E., Day, N., Noble, W.S. and Stamatoyannopoulos, J.A. (2007) Identification of higher-order functional domains in the human ENCODE regions. Genome Res., 17, 917-927.
24. Percival, D.B. and Walden, A.T. (2000) Wavelet Methods for Time Series Analysis. Cambridge University Press, Cambridge; New York.
25. Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate - a practical and powerful approach to multiple testing. J. R. Stat. Soc. B Methodol., 57, 289-300.
26. Chang, C.W., Cheng, W.C., Chen, C.R., Shu, W.Y., Tsai, M.L., Huang, C.L. and Hsu, I.C. (2011) Identification of human housekeeping genes and tissue-selective genes by microarray metaanalysis. PLoS One, 6, e22859.
27. Ernst, J. and Bar-Joseph, Z. (2006) STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics, 7, 191.
28. Stark, C., Breitkreutz, B.J., Reguly, T., Boucher, L., Breitkreutz, A. and Tyers, M. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res., 34, D535-D539.
29. Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M. and Haussler, D. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
30. Hindorff, L.A., Sethupathy, P., Junkins, H.A., Ramos, E.M., Mehta, J.P., Collins, F.S. and Manolio, T.A. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA, 106, 9362-9367.
31. Maston, G.A., Evans, S.K. and Green, M.R. (2006) Transcriptional regulatory elements in the human genome. Annu. Rev. Genomics Hum. Genet., 7, 29-59.
32. Rowley, J.D. (1973) Letter: a new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. Nature, 243, 290-293.
33. Deininger, M.W., Goldman, J.M. and Melo, J.V. (2000) The molecular biology of chronic myeloid leukemia. Blood, 96, 3343-3356.
34. Wong, N., Lai, P., Pang, E., Leung, T.W., Lau, J.W. and Johnson, P.J. (2000) A comprehensive karyotypic study on human hepatocellular carcinoma by spectral karyotyping. Hepatology, 32, 1060-1068.
35. Juran, B.D., Hirschfield, G.M., Invernizzi, P., Atkinson, E.J., Li, Y., Xie, G., Kosoy, R., Ransom, M., Sun, Y., Bianchi, I. et al. (2012) Immunochip analyses identify a novel risk locus for primary biliary cirrhosis at 13q14, multiple independent associations at four established risk loci and epistasis between 1p31 and 7q32 risk variants. Hum. Mol. Genet., 21, 5209-5221.
36. Koffler, D., Agnello, V., Thoburn, R. and Kunkel, H.G. (1971) Systemic lupus erythematosus: prototype of immune complex nephritis in man. J. Exp. Med., 134, 169-179.
37. Firestein, G.S. (2003) Evolving concepts of rheumatoid arthritis. Nature, 423, 356-361.
38. Thurman, R.E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M.T., Haugen, E., Sheffield, N.C., Stergachis, A.B., Wang, H., Vernot, B. et al. (2012) The accessible chromatin landscape of the human genome. Nature, 489, 75-82.
39. He, H.H., Meyer, C.A., Chen, M.W., Jordan, V.C., Brown, M. and Liu, X.S. (2012) Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res., 22, 1015-1025.
40. Gorkin, D.U., Lee, D., Reed, X., Fletez-Brant, C., Bessling, S.L., Loftus, S.K., Beer, M.A., Pavan, W.J. and McCallion, A.S. (2012) Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes. Genome Res., 22, 2290-2301.
41. Druker, B.J., Tamura, S., Buchdunger, E., Ohno, S., Segal, G.M., Fanning, S., Zimmermann, J. and Lydon, N.B. (1996) Effects of a selective inhibitor of the Abl tyrosine kinase on the growth of Bcr-Abl positive cells. Nat. Med., 2, 561-566.
42. Ren, R. (2005) Mechanisms of BCR-ABL in the pathogenesis of chronic myelogenous leukaemia. Nat. Rev. Cancer, 5, 172-183.
43. Mikkelsen, T.S., Ku, M., Jaffe, D.B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.K., Koche, R.P. et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 448, 553-560.
44. Yang, T., Espenshade, P.J., Wright, M.E., Yabe, D., Gong, Y., Aebersold, R., Goldstein, J.L. and Brown, M.S. (2002) Crucial step in cholesterol homeostasis: sterols promote binding of SCAP to INSIG-1, a membrane protein that facilitates retention of SREBPs in ER. Cell, 110, 489-500.
45. Janowski, B.A. (2002) The hypocholesterolemic agent LY295427 up-regulates INSIG-1, identifying the INSIG-1 protein as a mediator of cholesterol homeostasis through SREBP. Proc. Natl Acad. Sci. USA, 99, 12675-12680.
46. Xu, H., Wei, C.L., Lin, F. and Sung, W.K. (2008) An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics, 24, 2344-2349.
47. Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S.A., Flynn, R.A. and Wysocka, J. (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature, 470, 279-283.
48. Bernstein, B.E., Kamal, M., Lindblad-Toh, K., Bekiranov, S., Bailey, D.K., Huebert, D.J., McMahon, S., Karlsson, E.K., Kulbokas, E.J. 3rd, Gingeras, T.R. et al. (2005) Genomic maps and comparative analysis of histone modifications in human and mouse. Cell, 120, 169-181.
49. Lee, B.K., Bhinge, A.A., Battenhouse, A., McDaniell, R.M., Liu, Z., Song, L., Ni, Y., Birney, E., Lieb, J.D., Furey, T.S. et al. (2012) Celltype specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Res., 22, 9-24.
50. Dunham, I., Kundaje, A., Aldred, S.F., Collins, P.J., Davis, C.A., Doyle, F., Epstein, C.B., Frietze, S., Harrow, J., Kaul, R. et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
51. Celniker, S.E., Dillon, L.A., Gerstein, M.B., Gunsalus, K.C., Henikoff, S., Karpen, G.H., Kellis, M., Lai, E.C., Lieb, J.D., MacAlpine, D.M. et al. (2009) Unlocking the secrets of the genome. Nature, 459, 927-930.
52. Bernstein, B.E., Stamatoyannopoulos, J.A., Costello, J.F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M.A., Beaudet, A.L., Ecker, J.R. et al. (2010) The NIH roadmap epigenomics mapping consortium. Nat. Biotechnol., 28, 1045-1048.