Mapping E. coli RNA polymerase and associated transcription factors and identifying promoters genome-wide

Methods in Enzymology

Volumn 498, Issue , 2011, Pages 449-471

  Davis, Sarah E ^a   Mooney, Rachel A ^a   Kanin, Elenita I ^a   Grass, Jeff ^a   Landick, Robert ^a   Ansari, Aseem Z ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FORMALDEHYDE; RNA POLYMERASE; TRANSCRIPTION FACTOR;

ARTICLE; CELL GROWTH; CHROMATIN IMMUNOPRECIPITATION; ESCHERICHIA COLI; GENE CONTROL; GENE MAPPING; GENETIC TRANSCRIPTION; GENOME ANALYSIS; PRIORITY JOURNAL; PROMOTER REGION;

ESCHERICHIA COLI; MAMMALIA;

EID: 79957519168     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-385120-8.00020-6     Document Type: Chapter

References (30)

1. T.E. Allen, M.J. Herrgard, M. Liu, Y. Qiu, J.D. Glasner, F.R. Blattner, and B.O. Palsson Genome-scale analysis of the uses of the Escherichia coli genome: Model-driven analysis of heterogeneous data sets J. Bacteriol. 185 2003 6392 6399 (Pubitemid 37305539)
2. O. Aparicio, J.V. Geisberg, E. Sekinger, A. Yang, Z. Moqtaderi, and K. Struhl Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo F.M. Ausubel, R. Brent, R.E. Kingston, D.D. Moore, J.G. Seidman, J.A. Smith, K. Struhl, Current Protocols in Molecular Biology 2005 John Wiley & Sons, Inc. Hoboken, NJ 21.3.1 21.3.33
3. R.K. Auerbach, G. Euskirchen, J. Rozowsky, N. Lamarre-Vincent, Z. Moqtaderi, P. Lefrancois, K. Struhl, M. Gerstein, and M. Snyder Mapping accessible chromatin regions using Sono-Seq Proc. Natl. Acad. Sci. USA 106 2009 14926 14931
4. M.J. Buck, and J.D. Lieb ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments Genomics 83 2004 349 360 (Pubitemid 38220840)
5. M.J. Buck, A.B. Nobel, and J.D. Lieb ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data Genome Biol. 6 11 2005 R79
6. E.A. Campbell, N. Korzheva, A. Mustaev, K. Murakami, S. Nair, A. Goldfarb, and S.A. Darst Structural mechanism for rifampicin inhibition of bacterial RNA polymerase Cell 104 2001 901 912 (Pubitemid 32289282)
7. L. Gautier, L. Cope, B.M. Bolstad, and R.A. Irizarry Bioinformatics 2004 Oxford England 307 315 Vol. 20
8. D.C. Grainger, T.W. Overton, N. Reppas, J.T. Wade, E. Tamai, J.L. Hobman, C. Constantinidou, K. Struhl, G. Church, and S.J.W. Busby Genomic studies with Escherichia coli MelR protein: Application of chromatin immunoprecipitation and microarrays J. Bacteriol. 186 2004 6938 6943 (Pubitemid 39332133)
9. D.C. Grainger, D. Hurd, M. Harrison, J. Holdstock, and S.J.W. Busby Studies of the distribution of Escherichia coli camp-receptor protein and RNA polymerase along the E. coli chromosome Proc. Natl. Acad. Sci. USA 102 49 2005 17693 17698 (Pubitemid 41803559)
10. C.D. Herring, and F.R. Blattner Global transcriptional effects of a suppressor tRNA and the inactivation of the regulator frmR J. Bacteriol. 186 2004 6714 6720 (Pubitemid 39332108)
11. C.D. Herring, J.D. Glasner, and F.R. Blattner Gene replacement without selection: Regulated suppression of amber mutations in Escherichia coli Gene 311 2003 153 163 (Pubitemid 36830812)
12. C.D. Herring, M. Raffaelle, T.E. Allen, E.I. Kanin, R. Landick, A.Z. Ansari, and B.O. Palsson Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays J. Bacteriol. 187 2005 6166 6174 (Pubitemid 41262813)
13. D. Hoaglin, F. Mosteller, and J. Tukey Understanding Robust and Exploratory Data Analysis 2000 Wiley New York
14. V.R. Iyer, C.E. Horak, C.S. Scafe, D. Botstein, M. Synder, and P.O. Brown Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF Nature 409 2001 533 538 (Pubitemid 32144361)
15. E.I. Kanin, R.T. Kipp, C. Kung, M. Slattery, A. Viale, S. Hahn, K.M. Shokat, and A.Z. Ansari Chemical inhibition of the TFIIH-associated kinase Cdk7/Kin28 does not impair global mRNA synthesis Proc. Natl. Acad. Sci. USA 104 2007 5812 5817 (Pubitemid 47175616)
16. D.C.H. Lin, and A.D. Grossman Identification and characterization of a bacterial chromosome partitioning site Cell 92 1998 675 685 (Pubitemid 28141516)
17. W.R. McClure, and C.L. Cech On the mechanism of rifampicin inhibition of RNA systhesis J. Biol. Chem. 253 1978 8949 8956 (Pubitemid 9117005)
18. R.A. Mooney, S.E. Davis, J.M. Peters, J.L. Rowland, A.Z. Ansari, and R. Landick Regulator trafficking on bacterial transcription units in vivo Mol. Cell 33 2009 97 108
19. J.M. Peters, R.A. Mooney, P.F. Kuan, J.L. Rowland, S. Keles, and R. Landick Rho directs widspread termination of intragenic and stable RNA transcription Proc. Natl. Acad. Sci. USA 106 36 2009 15406 15411
20. R Development Core Team R: A language and environment for statistical computing 2005 R Foundation for Statistical Computing Vienna, Austria 3-900051-07-0 http://www.R-project.org
21. M. Raffaelle, E.I. Kanin, J. Vogt, R.R. Burgess, and A.Z. Ansari Holoenzyme switching and stochastic release of sigma factors from RNA polymerase in vivo Mol. Cell 20 2005 357 366 (Pubitemid 41572293)
22. B. Ren, F. Robert, J.J. Wyrick, O. Aparicio, E.G. Jennings, I. Simon, J. Zeitlinger, J. Schreiber, N. Hannett, E.I. Kanin, T.L. Volkert, and C.J. Wilson Genome-wide location and function of DNA binding proteins Science 290 2000 2306 2309 (Pubitemid 32041573)
23. N.B. Reppas, J.T. Wade, G.M. Church, and K. Struhl The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting Mol. Cell 24 2006 747 757 (Pubitemid 44839217)
24. D.N. Roberts, A.J. Stewart, J.T. Huff, and B.R. Cairns The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships Proc. Natl. Acad. Sci. USA 100 2003 14695 14700 (Pubitemid 37517953)
25. A. Sippel, and G. Hartmann Mode of action of rifampicin on the RNA polymerase reaction Biochem. Biophys. Acta. 157 1968 218 219
26. G. Smyth R. Gentleman, V. Carey, S.S. Dudoit, R. Irizarry, W. Huber, Bioinformatics and Computational Biology Solutions using R and Bioconductor 2005 Springer New York 397 420
27. G. Smyth, and T. Speed Normalization of cDNA microarray data Methods 31 2003 265 273 (San Diego, Calif,) (Pubitemid 37338763)
28. M.J. Solomon, and A. Varshavsky Formaldehyde-mediated DNA-protein crosslinking: A probe for in vivo chromatin structures Proc. Natl. Acad. Sci. USA 82 19 1985 6470 6474 (Pubitemid 16230535)
29. J.T. Wade, and K. Struhl Association of RNA polymerase with transcribed regions in Escherichia coli Proc. Natl. Acad. Sci. USA 101 2004 17777 17782 (Pubitemid 40051963)
30. Y.H. Yang, S. Dudoit, P. Luu, D.M. Lin, V. Peng, J. Ngai, and T.P. Speed Nucleic Acids Res. 30 2002 e15