Integrator complex regulates NELF-mediated RNA polymerase II pause/release and processivity at coding genes.

Bernd Stadelmayer,Bernd Stadelmayer,Bernd Stadelmayer,Bernd Stadelmayer,Raoul Raffel,Raoul Raffel,Stéphanie Rialle,Pascal Martin,Pascal Martin,Pascal Martin,Bijan Sobhian,Dany Severac,Gaël Micas,Gaël Micas,Slavik Koval,Nathalie Malirat,Hugues Parrinello,Adrien Gamot,Adrien Gamot,Olivier Cuvier,Olivier Cuvier,Olivier Cuvier,Olivier Cuvier,Monsef Benkirane,Monsef Benkirane,Monsef Benkirane,Monsef Benkirane

doi:10.1038/ncomms6531

Abstract

RNA polymerase II (RNAPII) pausing/termination shortly after initiation is a hallmark of gene regulation. Here, we show that negative elongation factor (NELF) interacts with Integrator complex subunits (INTScom), RNAPII and Spt5. The interaction between NELF and INTScom subunits is RNA and DNA independent. Using both human immunodeficiency virus type 1 promoter and genome-wide analyses, we demonstrate that Integrator subunits specifically control NELF-mediated RNAPII pause/release at coding genes. The strength of RNAPII pausing is determined by the nature of the NELF-associated INTScom subunits. Interestingly, in addition to controlling RNAPII pause-release INTS11 catalytic subunit of the INTScom is required for RNAPII processivity. Finally, INTScom target genes are enriched in human immunodeficiency virus type 1 transactivation response element/NELF binding element and in a 3' box sequence required for small nuclear RNA biogenesis. Revealing these unexpected functions of INTScom in regulating RNAPII pause-release and completion of mRNA synthesis of NELF-target genes will contribute to our understanding of the gene expression cycle.

Highlights

RNA polymerase II (RNAPII) pausing/termination shortly after initiation is a hallmark of gene regulation
Flag-HA IPed materials were run on SDS– polyacrylamide gel electrophoresis (SDS–PAGE) and proteins were visualised by silver staining and identified by mass spectrometry (MS) (Fig. 1a and Supplementary Dataset 1)
We found that RPB1 associated with eNELF-E is phosphorylated on Ser[7] but not on Serine 2 or Ser[5] (Fig. 1b and Supplementary Fig. 1A)

Summary

Introduction

RNA polymerase II (RNAPII) pausing/termination shortly after initiation is a hallmark of gene regulation. The interaction between NELF and INTScom subunits is RNA and DNA independent Using both human immunodeficiency virus type 1 promoter and genome-wide analyses, we demonstrate that Integrator subunits control NELF-mediated RNAPII pause/release at coding genes. INTScom target genes are enriched in human immunodeficiency virus type 1 transactivation response element/NELF binding element and in a 3’ box sequence required for small nuclear RNA biogenesis Revealing these unexpected functions of INTScom in regulating RNAPII pause-release and completion of mRNA synthesis of NELF-target genes will contribute to our understanding of the gene expression cycle. For protein coding genes P-TEFb-mediated phosphorylation of CTD at Serine 2 (Ser2) has been shown to have a key role in RNAPII pause-release and in coordinating/ coupling transcription elongation to RNA processing, including splicing, 3’end processing and termination of transcription[11,12]. Our study reveals an unexpected function of INTScom in regulating RNAPII pausing and processivity at coding genes

Methods

Results

Conclusion