Integrator Regulates Transcriptional Initiation and Pause Release following Activation

Abstract

SUMMARY Determining the factors regulating the rate limiting steps in transcriptional control is of fundamental importance to understanding the mechanisms that govern eukaryotic transcription. While studies in unicellular organisms have pointed to initiation as the rate-limiting step in transcription, a large body of work in metazoans indicates that the transition to productive transcriptional elongation may also constitute a critical step. Here, we show that the RNA polymerase II (RNAPII)-associated multi-protein complex, Integrator, plays a critical role in both initiation and the release of paused RNAPII in immediate early genes (IEGs) following transcriptional activation by epidermal growth factor (EGF) in human cells. Integrator is recruited to the IEGs in a signal-dependent manner and is required to engage the super elongation complex (SEC) in pause release. We propose a role for Integrator as an RNAPII-associated factor modulating both initiation and pause release during transcriptional activation in metazoans.

O-GlcNAcase Is an RNA Polymerase II Elongation Factor Coupled to Pausing Factors SPT5 and TIF1β

“…Release of the paused polymerase is achieved with P-TEFb phosphorylation of DSIF and NELF, ejecting NELF from pol II and converting DSIF into a positive elongation factor (14,15). The more recent discoveries of additional factors likely involved in pause establishment and release include human capping enzyme (16), the TFIIH-associated kinase, CDK7 (17,18), the TFIIH ERCC3 helicase (19), Mediator (20 -22), Integrator (23,24), ELL (25), TFIIS (26), TRIM28-KAP1-TIF1␤ (27,28), Top1 (29), SEC (30), PAF complex (31,32), and Gdown1 (33). The plethora of factors suggests that more complicated dynamics are at play in regulating pausing and elongation.…”

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

“…Other than processing the 3 ′ end of snRNAs, Integrator is also implicated in Pol II pause release and transcription elongation (Gardini et al 2014;Yamamoto et al 2014). To distinguish whether the reduced miRNA levels in the absence of Int11 are due to a processing or a transcriptional defect, we carried out RNase protection assays (RPAs) by annealing 32 P-body-labeled RNA probes complementary to pri-miR-HSUR4 with total RNA from transfected 293T cells and digesting with single-strand-specific RNases (Fig.…”

“…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.…”

Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions

“…Recent studies indicate that RNA-binding proteins can be associated with specific portions of chromatin, in part because of their interaction with RNA species associated with the transcriptional machinery (34,35). For example, the integrator complex, an snRNA-processing machinery, can be detected at the gene promoters, where it contributes to the regulation of transcriptional initiation and pause release (36). The RNA-binding proteins observed in these chromatin preparations included the RNA helicase DHX40, the RNA-capping enzyme RNMT, the RNA-decapping enzyme DCPS, the RNA cleavage factor CPSF3L, and many others.…”