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

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.

The host Integrator complex acts in transcription-independent maturation of herpesvirus microRNA 3′ ends

“…It would be interesting to examine whether there are stem-loop structures upstream of these 3 ′ box sequences. In the same study, Integrator was found to regulate transcription elongation at the HIV TAR element (Stadelmayer et al 2014), which forms a pre-miRNA-like stem-loop structure (Ouellet et al 2008). Integrator activity has also been implicated in the pausing of Pol II at the TAR element (Stadelmayer et al 2014).…”

“…Chromatin association analyses have shown that Integrator subunits bind to not only snRNA genes but also numerous protein-coding genes (Gardini et al 2014;Stadelmayer et al 2014;Skaar et al 2015). Intriguingly, when Stadelmayer et al (2014) analyzed Integrator-responsive mRNA genes, 40% were found to contain 3 ′ box-like sequences close to the transcription termination site (<1.5 kb). Moreover, the presence of a 3 ′ box was linked to a Pol II processivity defect over termination sites in Int11-depleted cells (Stadelmayer et al 2014).…”

“…Intriguingly, when Stadelmayer et al (2014) analyzed Integrator-responsive mRNA genes, 40% were found to contain 3 ′ box-like sequences close to the transcription termination site (<1.5 kb). Moreover, the presence of a 3 ′ box was linked to a Pol II processivity defect over termination sites in Int11-depleted cells (Stadelmayer et al 2014). It would be interesting to examine whether there are stem-loop structures upstream of these 3 ′ box sequences.…”

“…Since the discovery of Integrator as the long-sought factor in snRNA processing (Baillat et al 2005), new roles have been assigned to the Integrator complex: regulating RNA Pol II transcription promoter-proximal pausing as well as termination (Baillat and Wagner 2015). Chromatin association analyses have shown that Integrator subunits bind to not only snRNA genes but also numerous protein-coding genes (Gardini et al 2014;Stadelmayer et al 2014;Skaar et al 2015). Intriguingly, when Stadelmayer et al (2014) analyzed Integrator-responsive mRNA genes, 40% were found to contain 3 ′ box-like sequences close to the transcription termination site (<1.5 kb).…”

“…Therefore, initially, the Integrator complex was implicated in the 3 ′ end processing of small nuclear RNAs (snRNA), another class of abundant Pol II transcribed RNAs (Baillat et al 2005). Recent studies of Integrator have extended its functions into a broader spectrum of Pol II transcription events, including transcription initiation, promoter-proximal pausing, and termination of protein-coding transcripts (Gardini et al 2014;Stadelmayer et al 2014;Skaar et al 2015). In addition, Integrator is involved in microRNA (miRNA) biogenesis in Herpesvirus saimiri (HVS), a γ-herpesvirus that causes fatal T-cell leukemias and lymphomas in new world primates (Fickenscher and Fleckenstein 2001;Cazalla et al 2011). miRNAs are short (∼22-nucleotide [nt]) RNA molecules that control gene expression at the post-transcriptional level.…”