title: RNA polymerase II pausing can be retained or acquired during activation of genes involved in the epithelial to mesenchymal transition.
abstract: Promoter-proximal RNA polymerase II (Pol II) pausing is implicated in the regulation of gene transcription. However, the mechanisms of pausing including its dynamics during transcriptional responses remain to be fully understood. We performed global analysis of short capped RNAs and Pol II Chromatin Immunoprecipitation sequencing in MCF-7 breast cancer cells to map Pol II pausing across the genome, and used permanganate footprinting to specifically follow pausing during transcriptional activation of several genes involved in the epithelial to mesenchymal transition (EMT). We find that the gene for EMT master regulator Snail (SNAI1), but not Slug (SNAI2), shows evidence of Pol II pausing before activation. Transcriptional activation of the paused SNAI1 gene is accompanied by a further increase in Pol II pausing signal, whereas activation of non-paused SNAI2 gene results in the acquisition of a typical pausing signature. The increase in pausing signal reflects increased transcription initiation without changes in Pol II pausing. Activation of the heat shock HSP70 gene involves pausing release that speeds up Pol II turnover, but does not change pausing location. We suggest that Pol II pausing is retained during transcriptional activation and can further undergo regulated release in a signal-specific manner.
authors.affiliation: Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA.
authors.forename: Ann
authors.initials: A
authors.lastname: Samarakkody
authors.affiliation: Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA.
authors.forename: Ata
authors.initials: A
authors.lastname: Abbas
authors.affiliation: Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Scheidegger
authors.affiliation: Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA.
authors.forename: Jessica
authors.initials: J
authors.lastname: Warns
authors.affiliation: Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA.
authors.forename: Oscar
authors.initials: O
authors.lastname: Nnoli
authors.affiliation: Department of Computer Sciences, University of North Dakota, Grand Forks, ND 58202, USA.
authors.forename: Bradley
authors.initials: B
authors.lastname: Jokinen
authors.affiliation: Department of Computer Sciences, University of North Dakota, Grand Forks, ND 58202, USA.
authors.forename: Kris
authors.initials: K
authors.lastname: Zarns
authors.affiliation: Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA.
authors.forename: Brooke
authors.initials: B
authors.lastname: Kubat
authors.affiliation: Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA.
authors.forename: Archana
authors.initials: A
authors.lastname: Dhasarathy
authors.affiliation: Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA sergei.nechaev@med.und.edu.
authors.forename: Sergei
authors.initials: S
authors.lastname: Nechaev
mesh_terms: D058750:Epithelial-Mesenchymal Transition / Q000235:genetics*; D018840:HSP70 Heat-Shock Proteins / Q000235:genetics; D006801:Humans; D061986:MCF-7 Cells; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000378:metabolism*; D000071250:Snail Family Transcription Factors; D014157:Transcription Factors / Q000235:genetics; D015533:Transcriptional Activation
chemical_list: D018840:HSP70 Heat-Shock Proteins; C000604407:SNAI1 protein, human; C000604408:SNAI2 protein, human; D000071250:Snail Family Transcription Factors; D014157:Transcription Factors; D012319:RNA Polymerase II
references.citation: Genes Dev. 2012 May 1;26(9):933-44
references.pmid: 22549956
references.citation: Nat Rev Mol Cell Biol. 2012 Sep;13(9):543-7
references.pmid: 22895430
references.citation: Annu Rev Cell Dev Biol. 2011;27:347-76
references.pmid: 21740232
references.citation: Cell Stem Cell. 2008 Nov 6;3(5):480-3
references.pmid: 18983963
references.citation: Elife. 2014;3:e02407
references.pmid: 24843027
references.citation: Cell Rep. 2012 Oct 25;2(4):1025-35
references.pmid: 23062713
references.citation: Nat Genet. 2014 Dec;46(12):1311-20
references.pmid: 25383968
references.citation: Cancer Res. 2002 Mar 15;62(6):1613-8
references.pmid: 11912130
references.citation: Genes Dev. 2014 Jan 1;28(1):14-9
references.pmid: 24395245
references.citation: Proc Natl Acad Sci U S A. 1991 Sep 15;88(18):8052-6
references.pmid: 1896450
references.citation: Genes Dev. 2011 Apr 1;25(7):742-54
references.pmid: 21460038
references.citation: Sci Rep. 2015;5:8171
references.pmid: 25639887
references.citation: J Clin Invest. 2009 Jun;119(6):1420-8
references.pmid: 19487818
references.citation: Mol Cell Biol. 1986 Nov;6(11):3984-9
references.pmid: 3099167
references.citation: Science. 2008 Dec 19;322(5909):1845-8
references.pmid: 19056941
references.citation: Cancer Lett. 2012 Dec 28;325(2):117-24
references.pmid: 22750096
references.citation: Genes Dev. 2003 Jun 1;17(11):1402-14
references.pmid: 12782658
references.citation: Cancers (Basel). 2013 Dec 20;6(1):42-66
references.pmid: 24362507
references.citation: EMBO Rep. 2009 Sep;10(9):973-82
references.pmid: 19680288
references.citation: Genome Res. 2002 Jun;12(6):996-1006
references.pmid: 12045153
references.citation: Cell. 2013 May 23;153(5):976-87
references.pmid: 23706736
references.citation: Nat Genet. 2007 Dec;39(12):1507-11
references.pmid: 17994021
references.citation: Mol Cell. 2005 Jan 7;17(1):103-12
references.pmid: 15629721
references.citation: Mol Oncol. 2012 Dec;6(6):637-56
references.pmid: 23141799
references.citation: Nat Cell Biol. 2000 Feb;2(2):84-9
references.pmid: 10655587
references.citation: Cell. 1999 Apr 2;97(1):41-51
references.pmid: 10199401
references.citation: Genes Dev. 2008 Jul 15;22(14):1921-33
references.pmid: 18628398
references.citation: Genes Dev. 1996 Jun 15;10(12):1479-90
references.pmid: 8666232
references.citation: Oncogene. 2009 Oct 8;28(40):3573-85
references.pmid: 19633685
references.citation: Cell Cycle. 2008 Jun 1;7(11):1539-44
references.pmid: 18469524
references.citation: Nat Neurosci. 2011 Jul;14(7):848-56
references.pmid: 21623364
references.citation: Ann Surg Oncol. 2005 Jun;12(6):488-96
references.pmid: 15864483
references.citation: Genome Biol. 2014;15(6):R85
references.pmid: 24972996
references.citation: Genes Dev. 2011 Nov 15;25(22):2387-97
references.pmid: 22085965
references.citation: Mol Cell Biol. 2000 Apr;20(8):2629-34
references.pmid: 10733565
references.citation: Curr Opin Oncol. 2013 Jan;25(1):76-84
references.pmid: 23197193
references.citation: PLoS One. 2011;6(10):e26514
references.pmid: 22028892
references.citation: Cell. 1988 Sep 9;54(6):795-804
references.pmid: 3136931
references.citation: J Mammary Gland Biol Neoplasia. 2010 Jun;15(2):235-52
references.pmid: 20521089
references.citation: Cell Rep. 2014 Jul 24;8(2):514-27
references.pmid: 25043190
references.citation: Science. 2009 Jul 24;325(5939):471-3
references.pmid: 19628867
references.citation: Cell. 2011 May 13;145(4):622-34
references.pmid: 21549415
references.citation: Future Oncol. 2011 Feb;7(2):263-83
references.pmid: 21345145
references.citation: Genome Res. 2004 Jun;14(6):1188-90
references.pmid: 15173120
references.citation: Biochim Biophys Acta. 2011 Mar;1813(3):438-47
references.pmid: 21237216
references.citation: Nature. 2012 Mar 15;483(7389):295-301
references.pmid: 22258509
references.citation: Mol Cell. 2013 Jun 6;50(5):711-22
references.pmid: 23746353
references.citation: Mol Cancer Ther. 2009 Oct;8(10):2780-90
references.pmid: 19808979
references.citation: Hepatology. 2010 Sep;52(3):1033-45
references.pmid: 20564330
references.citation: Mol Endocrinol. 2007 Dec;21(12):2907-18
references.pmid: 17761946
references.citation: Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10460-5
references.pmid: 21670248
references.citation: PLoS One. 2012;7(9):e45045
references.pmid: 23024790
references.citation: Nucleic Acids Res. 2002 Jan 1;30(1):207-10
references.pmid: 11752295
references.citation: Cancer Res. 2013 Jan 1;73(1):235-45
references.pmid: 23054398
references.citation: Nat Chem Biol. 2011 Mar;7(3):182-8
references.pmid: 21278739
references.citation: Mol Cell Biol. 1991 Oct;11(10):5285-90
references.pmid: 1922045
references.citation: Breast Cancer Res. 2004;6(3):R215-31
references.pmid: 15084245
references.citation: Genome Biol. 2009;10(3):R25
references.pmid: 19261174
references.citation: Nature. 2006 Aug 31;442(7106):1050-3
references.pmid: 16929308
references.citation: Genes Dev. 2015 Jan 1;29(1):39-47
references.pmid: 25561494
references.citation: Mol Cell. 2013 Nov 21;52(4):517-28
references.pmid: 24184211
references.citation: Invest New Drugs. 2010 Dec;28 Suppl 1:S3-20
references.pmid: 21161327
references.citation: Gene. 1981 Oct;15(1):67-80
references.pmid: 6795091
references.citation: J Cell Sci. 2003 Feb 1;116(Pt 3):499-511
references.pmid: 12508111
references.citation: Cell. 2015 Jan 29;160(3):381-92
references.pmid: 25635454
references.citation: PLoS Comput Biol. 2011 May;7(5):e1001136
references.pmid: 21589887
references.citation: Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):10598-603
references.pmid: 24994903
references.citation: Cancer. 2005 Apr 15;103(8):1631-43
references.pmid: 15742334
references.citation: Cell. 2010 Nov 12;143(4):540-51
references.pmid: 21074046
references.citation: Science. 2010 Jan 15;327(5963):335-8
references.pmid: 20007866
references.citation: Nat Protoc. 2008;3(6):1077-84
references.pmid: 18536652
references.citation: Nat Rev Genet. 2012 Oct;13(10):720-31
references.pmid: 22986266
references.citation: Genes Dev. 1989 Nov;3(11):1814-22
references.pmid: 2558048
references.citation: Mol Cell Biol. 2011 Oct;31(20):4232-43
references.pmid: 21859888
references.citation: Mol Cell. 2013 Apr 25;50(2):212-22
references.pmid: 23523369
references.citation: Mol Cell. 2014 Oct 2;56(1):128-39
references.pmid: 25201415
references.citation: Methods. 2009 Aug;48(4):368-74
references.pmid: 19272453