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Items: 1 to 20 of 76

1.

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

Mokry M, Hatzis P, Schuijers J, Lansu N, Ruzius FP, Clevers H, Cuppen E.

Nucleic Acids Res. 2012 Jan;40(1):148-58. doi: 10.1093/nar/gkr720. Epub 2011 Sep 13.

2.

Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters.

Kininis M, Chen BS, Diehl AG, Isaacs GD, Zhang T, Siepel AC, Clark AG, Kraus WL.

Mol Cell Biol. 2007 Jul;27(14):5090-104. Epub 2007 May 21.

3.

RNA polymerase II pausing downstream of core histone genes is different from genes producing polyadenylated transcripts.

Anamika K, Gyenis À, Poidevin L, Poch O, Tora L.

PLoS One. 2012;7(6):e38769. doi: 10.1371/journal.pone.0038769. Epub 2012 Jun 11.

4.

Infection by Herpes Simplex Virus 1 Causes Near-Complete Loss of RNA Polymerase II Occupancy on the Host Cell Genome.

Abrisch RG, Eidem TM, Yakovchuk P, Kugel JF, Goodrich JA.

J Virol. 2015 Dec 16;90(5):2503-13. doi: 10.1128/JVI.02665-15. Erratum in: J Virol. 2016 Nov 28;90(24):11279.

5.

Close association of RNA polymerase II and many transcription factors with Pol III genes.

Raha D, Wang Z, Moqtaderi Z, Wu L, Zhong G, Gerstein M, Struhl K, Snyder M.

Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3639-44. doi: 10.1073/pnas.0911315106. Epub 2010 Feb 5.

6.

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression.

Reddy TE, Gertz J, Pauli F, Kucera KS, Varley KE, Newberry KM, Marinov GK, Mortazavi A, Williams BA, Song L, Crawford GE, Wold B, Willard HF, Myers RM.

Genome Res. 2012 May;22(5):860-9. doi: 10.1101/gr.131201.111. Epub 2012 Feb 2.

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9.

Postrecruitment regulation of RNA polymerase II directs rapid signaling responses at the promoters of estrogen target genes.

Kininis M, Isaacs GD, Core LJ, Hah N, Kraus WL.

Mol Cell Biol. 2009 Mar;29(5):1123-33. doi: 10.1128/MCB.00841-08. Epub 2008 Dec 22.

10.

Stably paused genes revealed through inhibition of transcription initiation by the TFIIH inhibitor triptolide.

Chen F, Gao X, Shilatifard A.

Genes Dev. 2015 Jan 1;29(1):39-47. doi: 10.1101/gad.246173.114.

11.

Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase.

Steinmetz EJ, Warren CL, Kuehner JN, Panbehi B, Ansari AZ, Brow DA.

Mol Cell. 2006 Dec 8;24(5):735-46.

12.

Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart.

He A, Kong SW, Ma Q, Pu WT.

Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5632-7. doi: 10.1073/pnas.1016959108. Epub 2011 Mar 17.

13.

Epigenetic regulation of human cis-natural antisense transcripts.

Conley AB, Jordan IK.

Nucleic Acids Res. 2012 Feb;40(4):1438-45. doi: 10.1093/nar/gkr1010.

14.

Nuclear RNA sequencing of the mouse erythroid cell transcriptome.

Mitchell JA, Clay I, Umlauf D, Chen CY, Moir CA, Eskiw CH, Schoenfelder S, Chakalova L, Nagano T, Fraser P.

PLoS One. 2012;7(11):e49274. doi: 10.1371/journal.pone.0049274. Epub 2012 Nov 29.

15.

Computer and statistical analysis of transcription factor binding and chromatin modifications by ChIP-seq data in embryonic stem cell.

Orlov Y, Xu H, Afonnikov D, Lim B, Heng JC, Yuan P, Chen M, Yan J, Clarke N, Orlova N, Huss M, Gunbin K, Podkolodnyy N, Ng HH.

J Integr Bioinform. 2012 Sep 18;9(2):211. doi: 10.2390/biecoll-jib-2012-211.

PMID:
22987856
16.

Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data.

Gupta R, Wikramasinghe P, Bhattacharyya A, Perez FA, Pal S, Davuluri RV.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S65. doi: 10.1186/1471-2105-11-S1-S65.

17.

A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.

He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.

PLoS One. 2009 Dec 1;4(12):e8155. doi: 10.1371/journal.pone.0008155.

18.

Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells.

Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL.

Mol Cell. 2013 Apr 25;50(2):212-22. doi: 10.1016/j.molcel.2013.02.015. Epub 2013 Mar 21. Erratum in: Mol Cell. 2013 Jun 6;50(5):778.

19.

Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

wa Maina C, Honkela A, Matarese F, Grote K, Stunnenberg HG, Reid G, Lawrence ND, Rattray M.

PLoS Comput Biol. 2014 May 15;10(5):e1003598. doi: 10.1371/journal.pcbi.1003598. eCollection 2014 May.

20.

ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands.

Welboren WJ, van Driel MA, Janssen-Megens EM, van Heeringen SJ, Sweep FC, Span PN, Stunnenberg HG.

EMBO J. 2009 May 20;28(10):1418-28. doi: 10.1038/emboj.2009.88. Epub 2009 Apr 4.

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