Literature DB >> 28860207

PAF1 regulation of promoter-proximal pause release via enhancer activation.

Fei Xavier Chen1, Peng Xie2, Clayton K Collings1, Kaixiang Cao1, Yuki Aoi1, Stacy A Marshall1, Emily J Rendleman1, Michal Ugarenko1, Patrick A Ozark1, Anda Zhang3, Ramin Shiekhattar3, Edwin R Smith1, Michael Q Zhang2,4, Ali Shilatifard5,6.   

Abstract

Gene expression in metazoans is regulated by RNA polymerase II (Pol II) promoter-proximal pausing and its release. Previously, we showed that Pol II-associated factor 1 (PAF1) modulates the release of paused Pol II into productive elongation. Here, we found that PAF1 occupies transcriptional enhancers and restrains hyperactivation of a subset of these enhancers. Enhancer activation as the result of PAF1 loss releases Pol II from paused promoters of nearby PAF1 target genes. Knockout of PAF1-regulated enhancers attenuates the release of paused Pol II on PAF1 target genes without major interference in the establishment of pausing at their cognate promoters. Thus, a subset of enhancers can primarily modulate gene expression by controlling the release of paused Pol II in a PAF1-dependent manner.
Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

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Year:  2017        PMID： 28860207      PMCID： PMC6055228          DOI： 10.1126/science.aan3269

Source DB:  PubMed          Journal:  Science        ISSN： 0036-8075            Impact factor:   47.728


  34 in total

1.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.

Authors:  Nathaniel D Heintzman; Rhona K Stuart; Gary Hon; Yutao Fu; Christina W Ching; R David Hawkins; Leah O Barrera; Sara Van Calcar; Chunxu Qu; Keith A Ching; Wei Wang; Zhiping Weng; Roland D Green; Gregory E Crawford; Bing Ren
Journal:  Nat Genet       Date:  2007-02-04       Impact factor: 38.330

2.  Inducible, reversible system for the rapid and complete degradation of proteins in mammalian cells.

Authors:  Andrew J Holland; Daniele Fachinetti; Joo Seok Han; Don W Cleveland
Journal:  Proc Natl Acad Sci U S A       Date:  2012-11-12       Impact factor: 11.205

3.  c-Myc regulates transcriptional pause release.

Authors:  Peter B Rahl; Charles Y Lin; Amy C Seila; Ryan A Flynn; Scott McCuine; Christopher B Burge; Phillip A Sharp; Richard A Young
Journal:  Cell       Date:  2010-04-30       Impact factor: 41.582

4.  Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC).

Authors:  Chengqi Lin; Alexander S Garrett; Bony De Kumar; Edwin R Smith; Madelaine Gogol; Christopher Seidel; Robb Krumlauf; Ali Shilatifard
Journal:  Genes Dev       Date:  2011-07-15       Impact factor: 11.361

5.  KAP1 Recruitment of the 7SK snRNP Complex to Promoters Enables Transcription Elongation by RNA Polymerase II.

Authors:  Ryan P McNamara; Jonathan E Reeder; Elizabeth A McMillan; Curtis W Bacon; Jennifer L McCann; Iván D'Orso
Journal:  Mol Cell       Date:  2015-12-24       Impact factor: 17.970

6.  Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo.

Authors:  Mounia Lagha; Jacques P Bothma; Emilia Esposito; Samuel Ng; Laura Stefanik; Chiahao Tsui; Jeffrey Johnston; Kai Chen; David S Gilmour; Julia Zeitlinger; Michael S Levine
Journal:  Cell       Date:  2013-05-23       Impact factor: 41.582

7.  Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation.

Authors:  Bryan A Gibson; Yajie Zhang; Hong Jiang; Kristine M Hussey; Jonathan H Shrimp; Hening Lin; Frank Schwede; Yonghao Yu; W Lee Kraus
Journal:  Science       Date:  2016-06-02       Impact factor: 47.728

8.  BET Bromodomain Proteins Function as Master Transcription Elongation Factors Independent of CDK9 Recruitment.

Authors:  Georg E Winter; Andreas Mayer; Dennis L Buckley; Michael A Erb; Justine E Roderick; Sarah Vittori; Jaime M Reyes; Julia di Iulio; Amanda Souza; Christopher J Ott; Justin M Roberts; Rhamy Zeid; Thomas G Scott; Joshiawa Paulk; Kate Lachance; Calla M Olson; Shiva Dastjerdi; Sophie Bauer; Charles Y Lin; Nathanael S Gray; Michelle A Kelliher; L Stirling Churchman; James E Bradner
Journal:  Mol Cell       Date:  2017-06-29       Impact factor: 17.970

9.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.

Authors:  Bo Li; Colin N Dewey
Journal:  BMC Bioinformatics       Date:  2011-08-04       Impact factor: 3.307

10.  SET1A/COMPASS and shadow enhancers in the regulation of homeotic gene expression.

Authors:  Kaixiang Cao; Clayton K Collings; Stacy A Marshall; Marc A Morgan; Emily J Rendleman; Lu Wang; Christie C Sze; Tianjiao Sun; Elizabeth T Bartom; Ali Shilatifard
Journal:  Genes Dev       Date:  2017-05-09       Impact factor: 11.361
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  37 in total

Review 1.  Towards a comprehensive catalogue of validated and target-linked human enhancers.

Authors:  Molly Gasperini; Jacob M Tome; Jay Shendure
Journal:  Nat Rev Genet       Date:  2020-01-27       Impact factor: 53.242

Review 2.  Eukaryotic core promoters and the functional basis of transcription initiation.

Authors:  Vanja Haberle; Alexander Stark
Journal:  Nat Rev Mol Cell Biol       Date:  2018-10       Impact factor: 94.444

3.  SETDB1 mediated histone H3 lysine 9 methylation suppresses MLL-fusion target expression and leukemic transformation.

Authors:  James Ropa; Nirmalya Saha; Hsiangyu Hu; Luke F Peterson; Moshe Talpaz; Andrew G Muntean
Journal:  Haematologica       Date:  2019-09-26       Impact factor: 9.941

4.  Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods.

Authors:  Fei Sun; Constantinos Chronis; Michael Kronenberg; Xiao-Fen Chen; Trent Su; Fides D Lay; Kathrin Plath; Siavash K Kurdistani; Michael F Carey
Journal:  Mol Cell       Date:  2018-12-06       Impact factor: 17.970

Review 5.  Molecular mechanisms driving transcriptional stress responses.

Authors:  Anniina Vihervaara; Fabiana M Duarte; John T Lis
Journal:  Nat Rev Genet       Date:  2018-06       Impact factor: 53.242

6.  NELF Regulates a Promoter-Proximal Step Distinct from RNA Pol II Pause-Release.

Authors:  Yuki Aoi; Edwin R Smith; Avani P Shah; Emily J Rendleman; Stacy A Marshall; Ashley R Woodfin; Fei X Chen; Ramin Shiekhattar; Ali Shilatifard
Journal:  Mol Cell       Date:  2020-03-09       Impact factor: 17.970

7.  IL-1 Transcriptional Responses to Lipopolysaccharides Are Regulated by a Complex of RNA Binding Proteins.

Authors:  Lihua Shi; Li Song; Kelly Maurer; Ying Dou; Vishesh R Patel; Chun Su; Michelle E Leonard; Sumei Lu; Kenyaita M Hodge; Annabel Torres; Alessandra Chesi; Struan F A Grant; Andrew D Wells; Zhe Zhang; Michelle A Petri; Kathleen E Sullivan
Journal:  J Immunol       Date:  2020-01-17       Impact factor: 5.422

Review 8.  Nascent RNA analyses: tracking transcription and its regulation.

Authors:  Erin M Wissink; Anniina Vihervaara; Nathaniel D Tippens; John T Lis
Journal:  Nat Rev Genet       Date:  2019-08-09       Impact factor: 53.242

9.  Multivalent Role of Human TFIID in Recruiting Elongation Components at the Promoter-Proximal Region for Transcriptional Control.

Authors:  Dipika Yadav; Koushik Ghosh; Subham Basu; Robert G Roeder; Debabrata Biswas
Journal:  Cell Rep       Date:  2019-01-29       Impact factor: 9.423

10.  The Paf1 complex and P-TEFb have reciprocal and antagonist roles in maintaining multipotent neural crest progenitors.

Authors:  Michael J Jurynec; Xiaoying Bai; Brent W Bisgrove; Haley Jackson; Alex Nechiporuk; Rebecca A S Palu; Hannah A Grunwald; Yi-Chu Su; Kazuyuki Hoshijima; H Joseph Yost; Leonard I Zon; David Jonah Grunwald
Journal:  Development       Date:  2019-12-16       Impact factor: 6.868
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