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RNA Polymerase II Pausing Downstream of Core Histone Genes Is Different from Genes Producing Polyadenylated Transcripts

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  • Krishanpal Anamika
  • Àkos Gyenis
  • Laetitia Poidevin
  • Olivier Poch
  • Làszlò Tora

Abstract

Recent genome-wide chromatin immunoprecipitation coupled high throughput sequencing (ChIP-seq) analyses performed in various eukaryotic organisms, analysed RNA Polymerase II (Pol II) pausing around the transcription start sites of genes. In this study we have further investigated genome-wide binding of Pol II downstream of the 3′ end of the annotated genes (EAGs) by ChIP-seq in human cells. At almost all expressed genes we observed Pol II occupancy downstream of the EAGs suggesting that Pol II pausing 3′ from the transcription units is a rather common phenomenon. Downstream of EAGs Pol II transcripts can also be detected by global run-on and sequencing, suggesting the presence of functionally active Pol II. Based on Pol II occupancy downstream of EAGs we could distinguish distinct clusters of Pol II pause patterns. On core histone genes, coding for non-polyadenylated transcripts, Pol II occupancy is quickly dropping after the EAG. In contrast, on genes, whose transcripts undergo polyA tail addition [poly(A)+], Pol II occupancy downstream of the EAGs can be detected up to 4–6 kb. Inhibition of polyadenylation significantly increased Pol II occupancy downstream of EAGs at poly(A)+ genes, but not at the EAGs of core histone genes. The differential genome-wide Pol II occupancy profiles 3′ of the EAGs have also been confirmed in mouse embryonic stem (mES) cells, indicating that Pol II pauses genome-wide downstream of the EAGs in mammalian cells. Moreover, in mES cells the sharp drop of Pol II signal at the EAG of core histone genes seems to be independent of the phosphorylation status of the C-terminal domain of the large subunit of Pol II. Thus, our study uncovers a potential link between different mRNA 3′ end processing mechanisms and consequent Pol II transcription termination processes.

Suggested Citation

  • Krishanpal Anamika & Àkos Gyenis & Laetitia Poidevin & Olivier Poch & Làszlò Tora, 2012. "RNA Polymerase II Pausing Downstream of Core Histone Genes Is Different from Genes Producing Polyadenylated Transcripts," PLOS ONE, Public Library of Science, vol. 7(6), pages 1-14, June.
  • Handle: RePEc:plo:pone00:0038769
    DOI: 10.1371/journal.pone.0038769
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    References listed on IDEAS

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    1. Zhijin Wu & Rafael A. Irizarry & Robert Gentleman & Francisco Martinez-Murillo & Forrest Spencer, 2004. "A Model-Based Background Adjustment for Oligonucleotide Expression Arrays," Journal of the American Statistical Association, American Statistical Association, vol. 99, pages 909-917, December.
    2. Jean-Christophe Dantonel & Kanneganti G. K. Murthy & James L. Manley & Laszlo Tora, 1997. "Transcription factor TFIID recruits factor CPSF for formation of 3′ end of mRNA," Nature, Nature, vol. 389(6649), pages 399-402, September.
    3. Zhijin Wu & Rafael Irizarry & Robert Gentleman & Francisco Martinez Murillo & Forrest Spencer, 2004. "A Model Based Background Adjustment for Oligonucleotide Expression Arrays," Johns Hopkins University Dept. of Biostatistics Working Paper Series 1001, Berkeley Electronic Press.
    4. Mark Ptashne & Alexander Gann, 1997. "Transcriptional activation by recruitment," Nature, Nature, vol. 386(6625), pages 569-577, April.
    5. Minkyu Kim & Nevan J. Krogan & Lidia Vasiljeva & Oliver J. Rando & Eduard Nedea & Jack F. Greenblatt & Stephen Buratowski, 2004. "The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II," Nature, Nature, vol. 432(7016), pages 517-522, November.
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    1. Hidefumi Suzuki & Ryota Abe & Miho Shimada & Tomonori Hirose & Hiroko Hirose & Keisuke Noguchi & Yoko Ike & Nanami Yasui & Kazuki Furugori & Yuki Yamaguchi & Atsushi Toyoda & Yutaka Suzuki & Tatsuro Y, 2022. "The 3′ Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies’ association with histone locus bodies," Nature Communications, Nature, vol. 13(1), pages 1-24, December.

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