A co-localization model of paired ChIP-seq data using a large ENCODE data set enables comparison of multiple samples

Nucleic Acids Research

Volumn 41, Issue 1, 2013, Pages 54-62

  Maehara, Kazumitsu ^a,b   Odawara, Jun ^a   Harada, Akihito ^a   Yoshimi, Tomohiko ^c   Nagao, Koji ^d   Obuse, Chikashi ^d   Akashi, Koichi ^a   Tachibana, Taro ^c   Sakata, Toshio ^b   Ohkawa, Yasuyuki ^a  

^a KYUSHU UNIVERSITY   (Japan)

^b KYUSHU UNIVERSITY   (Japan)

^c Osaka Prefecture University   (Japan)

^d HOKKAIDO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE II; SERINE; TRANSCRIPTION FACTOR;

ANIMAL EXPERIMENT; ARTICLE; CARBOXY TERMINAL SEQUENCE; CHROMATIN IMMUNOPRECIPITATION; CHROMATIN IMMUNOPRECIPITATION BY SEQUENCING; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; ENCYCLOPEDIA OF DNA ELEMENTS; ENZYME ACTIVITY; ENZYME PHOSPHORYLATION; FEMALE; HELA CELL; HISTONE MODIFICATION; HUMAN; HUMAN CELL; IMMUNIZATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN LOCALIZATION; RAT;

CHROMATIN IMMUNOPRECIPITATION; EPIGENESIS, GENETIC; HELA CELLS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HISTONES; HUMANS; MODELS, GENETIC; PHOSPHORYLATION; RNA POLYMERASE II; SERINE; SOFTWARE; TRANSCRIPTION INITIATION SITE;

EID: 84871798675     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1010     Document Type: Article

References (28)

1. Park, P.J. (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat. Rev. Genet., 10, 669-680.
2. ENCODE Project Consortium. (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol., 9, e1001046+.
3. Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J. and Gray, M.W. (2005) The tree of eukaryotes. Trends Ecol. Evol., 20, 670-676.
4. Pepke, S., Wold, B. and Mortazavi, A. (2009) Computation for ChIP-seq and RNA-seq studies. Nat. Methods, 6, S22-S32.
5. Zhang, Z.D., Rozowsky, J., Snyder, M., Chang, J. and Gerstein, M. (2008) Modeling ChIP sequencing in silico with applications. PLoS Comput. Biol., 4, e1000158.
6. 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 ChIP-seq experiments relative to controls. Nat. Biotechnol., 27, 66-75.
7. Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W. et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.
8. Malone, B.M., Tan, F., Bridges, S.M. and Peng, Z. (2011) Comparison of four ChIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data. PLoS One, 6, e25260+.
9. Wilbanks, E.G. and Facciotti, M.T. (2010) Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One, 5, e11471.
10. Laajala, T.D., Raghav, S., Tuomela, S., Lahesmaa, R., Aittokallio, T. and Elo, L.L. (2009) A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics, 10, 618.
11. Harada, A., Okada, S., Konno, D., Odawara, J., Yoshimi, T., Yoshimura, S., Kumamaru, H., Saiwai, H., Tsubota, T., Kurumizaka, H. et al. (2012) Chd2 interacts with H3.3 to determine myogenic cell fate. EMBO J., 31, 2994-3007.
12. Mendoza-Parra, M.A., Sankar, M., Walia, M. and Gronemeyer, H. (2012) POLYPHEMUS: R package for comparative analysis of RNA polymerase II ChIP-seq profiles by non-linear normalization. Nucleic Acids Res., 40, e30.
13. Taslim, C., Wu, J., Yan, P., Singer, G., Parvin, J., Huang, T., Lin, S. and Huang, K. (2009) Comparative study on ChIP-seq data: normalization and binding pattern characterization. Bioinformatics, 25, 2334-2340.
14. Odawara, J., Harada, A., Yoshimi, T., Maehara, K., Tachibana, T., Okada, S., Akashi, K. and Ohkawa, Y. (2011) The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach. BMC Genomics, 12, 516.
15. Sado, Y., Kagawa, M., Kishiro, Y., Sugihara, K., Naito, I., Seyer, J.M., Sugimoto, M., Oohashi, T. and Ninomiya, Y. (1995) Establishment by the rat lymph node method of epitope-defined monoclonal antibodies recognizing the six different alpha chains of human type IV collagen. Histochem. Cell Biol., 104, 267-275.
16. Micsinai, M., Parisi, F., Strino, F., Asp, P., Dynlacht, B.D. and Kluger, Y. (2012) Picking ChIP-seq peak detectors for analyzing chromatin modification experiments. Nucleic Acids Res., 40, e70.
17. Brookes, E. and Pombo, A. (2009) Modifications of RNA polymerase II are pivotal in regulating gene expression states. EMBO Rep., 10, 1213-1219.
18. Cao, Y., Yao, Z., Sarkar, D., Lawrence, M., Sanchez, G.J., Parker, M.H., MacQuarrie, K.L., Davison, J., Morgan, M.T., Ruzzo, W.L. et al. (2010) Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev. Cell, 18, 662-674.
19. van Steensel, B., van Binnendijk, E.P., Hornsby, C.D., van der Voort, H.T., Krozowski, Z.S., de Kloet, E.R. and van Driel, R. (1996) Partial colocalization of glucocorticoid and mineralocorticoid receptors in discrete compartments in nuclei of rat hippocampus neurons. J. Cell Sci., 109, 787-792.
20. Jin, C., Zang, C., Wei, G., Cui, K., Peng, W., Zhao, K. and Felsenfeld, G. (2009) H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nat. Genet., 41, 941-945.
21. Goldberg, A.D., Banaszynski, L.A., Noh, K.-M.M., Lewis, P.W., Elsaesser, S.J., Stadler, S., Dewell, S., Law, M., Guo, X., Li, X. et al. (2010) Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell, 140, 678-691.
22. Li, J. and Gilmour, D.S. (2011) Promoter proximal pausing and the control of gene expression. Curr. Opin. Genet. Dev., 21, 231-235.
23. Marshall, N.F., Peng, J., Xie, Z. and Price, D.H. (1996) Control of RNA polymerase II elongation potential by a novel carboxyl-terminal domain kinase. J. Biol. Chem., 271, 27176-27183.
24. Mayer, A., Lidschreiber, M., Siebert, M., Leike, K., Soding, J. and Cramer, P. (2010) Uniform transitions of the general RNA polymerase II transcription complex. Nat. Struct. Mol. Biol., 17, 1272-1278.
25. Boeing, S., Rigault, C., Heidemann, M., Eick, D. and Meisterernst, M. (2010) RNA polymerase II C-terminal heptarepeat domain Ser-7 phosphorylation is established in a mediator-dependent fashion. J. Biol. Chem., 285, 188-196.
26. Dostie, J., Richmond, T.A., Arnaout, R.A., Selzer, R.R., Lee, W.L., Honan, T.A., Rubio, E.D., Krumm, A., Lamb, J., Nusbaum, C. et al. (2006) Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res., 16, 1299-1309.
27. Splinter, E., de Wit, E., van de Werken, H.J.G., Klous, P. and de Laat, W. (2012) Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation. Methods.
28. Edmunds, J.W., Mahadevan, L.C. and Clayton, A.L. (2008) Dynamic histone H3 methylation during gene induction: HYPB/Setd2 mediates all H3K36 trimethylation. EMBO J., 27, 406-420.