Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes

Nucleic Acids Research

Volumn 40, Issue 1, 2012, Pages 148-158

  Mokry, Michal ^a   Hatzis, Pantelis ^a   Schuijers, Jurian ^a   Lansu, Nico ^a   Ruzius, Frans Paul ^a   Clevers, Hans ^a   Cuppen, Edwin ^a  

^a UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BETA CATENIN; RNA; RNA POLYMERASE II; TRANSCRIPTION FACTOR; WNT PROTEIN;

ARTICLE; CANCER CELL CULTURE; COLON CANCER; CONTROLLED STUDY; ENZYME BINDING; GENE CONTROL; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE REGULATORY NETWORK; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; STEADY STATE;

CELL LINE, TUMOR; CHROMATIN IMMUNOPRECIPITATION; COLONIC NEOPLASMS; GENE EXPRESSION REGULATION; GENOMICS; HUMANS; RNA; RNA POLYMERASE II; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION FACTORS; WNT SIGNALING PATHWAY;

EID: 84855286233     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr720     Document Type: Article

References (37)

1. Shyu, A.B., Wilkinson, M.F. and van Hoof, A. (2008) Messenger RNA regulation: to translate or to degrade. EMBO J., 27, 471-481. (Pubitemid 351225677)
2. Raghavan, A., Ogilvie, R.L., Reilly, C., Abelson, M.L., Raghavan, S., Vasdewani, J., Krathwohl, M. and Bohjanen, P.R. (2002) Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes. Nucleic Acids Res., 30, 5529-5538. (Pubitemid 36113930)
3. Sharova, L.V., Sharov, A.A., Nedorezov, T., Piao, Y., Shaik, N. and Ko, M.S. (2009) Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells. DNA Res., 16, 45-58.
4. Wang, Y., Liu, C.L., Storey, J.D., Tibshirani, R.J., Herschlag, D. and Brown, P.O. (2002) Precision and functional specificity in mRNA decay. Proc. Natl Acad. Sci. USA, 99, 5860-5865. (Pubitemid 34493230)
5. Garcia-Martinez, J., Aranda, A. and Perez-Ortin, J.E. (2004) Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Mol. Cell, 15, 303-313. (Pubitemid 38950977)
6. Miller, C., Schwalb, B., Maier, K., Schulz, D., Dumcke, S., Zacher, B., Mayer, A., Sydow, J., Marcinowski, L., Dolken, L. et al. (2011) Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol. Syst. Biol., 7, 458.
7. Churchman, L.S. and Weissman, J.S. (2011) Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature, 469, 368-373.
8. Core, L.J., Waterfall, J.J. and Lis, J.T. (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science, 322, 1845-1848.
9. Mokry, M., Hatzis, P., de Bruijn, E., Koster, J., Versteeg, R., Schuijers, J., van de Wetering, M., Guryev, V., Clevers, H. and Cuppen, E. (2010) Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles. PLoS ONE, 5, e15092.
10. Adli, M., Zhu, J. and Bernstein, B.E. (2010) Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Nat. Methods, 7, 615-618.
11. Dahl, J.A. and Collas, P. (2008) A rapid micro chromatin immunoprecipitation assay (microChIP). Nat. Protoc., 3, 1032-1045. (Pubitemid 351818692)
12. Dahl, J.A. and Collas, P. (2008) MicroChIP-a rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies. Nucleic Acids Res., 36, e15.
13. Dahl, J.A., Reiner, A.H. and Collas, P. (2009) Fast genomic muChIP-chip from 1, 000 cells. Genome Biol., 10, R13.
14. Fanelli, M., Amatori, S., Barozzi, I., Soncini, M., Dal Zuffo, R., Bucci, G., Capra, M., Quarto, M., Dellino, G.I., Mercurio, C. et al. (2010) Pathology tissue-chromatin immunoprecipitation, coupled with high-throughput sequencing, allows the epigenetic profiling of patient samples. Proc. Natl Acad. Sci. USA, 107, 21535-21540.
15. van de Wetering, M., Oving, I., Muncan, V., Pon Fong, M.T., Brantjes, H., van Leenen, D., Holstege, F.C., Brummelkamp, T.R., Agami, R. and Clevers, H. (2003) Specific inhibition of gene expression using a stably integrated, inducible small-interfering-RNA vector. EMBO Rep., 4, 609-615. (Pubitemid 36939953)
16. Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B. and Speed, T.P. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res., 31, e15.
17. Li, H., Ruan, J. and Durbin, R. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18, 1851-1858.
18. Smyth, G. (2005) In Gentleman, R., Carey, V., Huber, W., Irizarry, R. and Dudoit, S. (eds), Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Springer, New York, pp. 397-420.
19. Hatzis, P., van der Flier, L.G., van Driel, M.A., Guryev, V., Nielsen, F., Denissov, S., Nijman, I.J., Koster, J., Santo, E.E., Welboren, W. et al. (2008) Genome-wide pattern of TCF7L2/ TCF4 chromatin occupancy in colorectal cancer cells. Mol. Cell. Biol., 28, 2732-2744. (Pubitemid 351542371)
20. Ji, H., Jiang, H., Ma, W., Johnson, D.S., Myers, R.M. and Wong, W.H. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol., 26, 1293-1300.
21. Myers, R.M., Stamatoyannopoulos, J., Snyder, M., Dunham, I., Hardison, R.C., Bernstein, B.E., Gingeras, T.R., Kent, W.J., Birney, E., Wold, B. et al. (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol., 9, e1001046.
22. Chen, X., Xu, H., Yuan, P., Fang, F., Huss, M., Vega, V.B., Wong, E., Orlov, Y.L., Zhang, W., Jiang, J. et al. (2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell, 133, 1106-1117. (Pubitemid 351787745)
23. Ouyang, Z., Zhou, Q. and Wong, W.H. (2009) ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc. Natl Acad. Sci. USA, 106, 21521-21526.
24. Development Core Team. (2009) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna.
25. Hastie, T., Tibshirani, R. and Friedman, J. (2003) The Elements of Statistical Learning: Data Mining, Inference, and Prediction. Springer, New York.
26. Therneau, T.M. and Atkinson, B. (2009) rpart: Recursive Partitioning. http://stat.ethz.ch/CRAN/.
27. Besse, S., Vigneron, M., Pichard, E. and Puvion-Dutilleul, F. (1995) Synthesis and maturation of viral transcripts in herpes simplex virus type 1 infected HeLa cells: the role of interchromatin granules. Gene Expr., 4, 143-161.
28. Korinek, V., Barker, N., Morin, P.J., van Wichen, D., de Weger, R., Kinzler, K.W., Vogelstein, B. and Clevers, H. (1997) Constitutive transcriptional activation by a beta-catenin-Tcf complex in APC-/-colon carcinoma. Science, 275, 1784-1787. (Pubitemid 27136714)
29. Graham, T.A., Weaver, C., Mao, F., Kimelman, D. and Xu, W. (2000) Crystal structure of a beta-catenin/Tcf complex. Cell, 103, 885-896.
30. He, T.C., Sparks, A.B., Rago, C., Hermeking, H., Zawel, L., da Costa, L.T., Morin, P.J., Vogelstein, B. and Kinzler, K.W. (1998) Identification of c-MYC as a target of the APC pathway. Science, 281, 1509-1512. (Pubitemid 28425575)
31. Kooren, J., Palstra, R.J., Klous, P., Splinter, E., von Lindern, M., Grosveld, F. and de Laat, W. (2007) Beta-globin active chromatin Hub formation in differentiating erythroid cells and in p45 NF-E2 knock-out mice. J. Biol. Chem., 282, 16544-16552. (Pubitemid 47100343)
32. Fullwood, M.J., Liu, M.H., Pan, Y.F., Liu, J., Xu, H., Mohamed, Y.B., Orlov, Y.L., Velkov, S., Ho, A., Mei, P.H. et al. (2009) An oestrogen-receptor- alpha-bound human chromatin interactome. Nature, 462, 58-64.
33. Rahl, P.B., Lin, C.Y., Seila, A.C., Flynn, R.A., McCuine, S., Burge, C.B., Sharp, P.A. and Young, R.A. (2010) c-Myc regulates transcriptional pause release. Cell, 141, 432-445.
34. 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.
35. Margaritis, T. and Holstege, F.C. (2008) Poised RNA polymerase II gives pause for thought. Cell, 133, 581-584. (Pubitemid 351636308)
36. Eden, E., Navon, R., Steinfeld, I., Lipson, D. and Yakhini, Z. (2009) GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics, 10, 48.
37. Anders, S. (2009) Visualization of genomic data with the Hilbert curve. Bioinformatics, 25, 1231-1235.