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Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE210880 | GEO | 2023/07/27

REPOSITORIES: GEO

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Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity [TT-seq]

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Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity [ChIP-seq]

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Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity

Project description:Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity

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Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity [ChIP-seq]

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Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity [TT-seq]

Project description:Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity [TT-seq]

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Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity [DRB/TT-seq]

Project description:Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity [DRB/TT-seq]

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Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window during elongation.

Project description:Spt5 is a highly conserved RNA polymerase II (Pol II)-associated pausing and elongation factor. However, its impact on global elongation and Pol II processivity in mammalian cells has not been clarified. Here, we show that depleting Spt5 in mouse embryonic fibroblasts (MEFs) does not cause global elongation defects or decreased elongation rates. Instead, in Spt5-depleted cells, a fraction of Pol II molecules are dislodged during elongation, thus decreasing the number of Pol II complexes that complete the transcription cycle. Most strikingly, this decrease is restricted to a narrow window between 15 and 20 kb from the promoter, a distance which coincides with the stage where accelerating Pol II attains maximum elongation speed. Consequently, long genes show a greater dependency on Spt5 for optimal elongation efficiency and overall gene expression than short genes. We propose that an important role of Spt5 in mammalian elongation is to promote the processivity of those Pol II complexes that are transitioning toward maximum elongation speed 15-20 kb from the promoter.

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

Project description: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.

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PARP1's Involvement in RNA Polymerase II Elongation: Pausing and Releasing Regulation through the Integrator and Super Elongation Complex.

Project description:RNA polymerase elongation along the gene body is tightly regulated to ensure proper transcription and alternative splicing events. Understanding the mechanism and factors critical in regulating the rate of RNA polymerase II elongation and processivity is clearly important. Recently we showed that PARP1, a well-known DNA repair protein, when bound to chromatin, regulates RNA polymerase II elongation. However, the mechanism by which it does so is not known. In the current study, we aimed to tease out how PARP1 regulates RNAPII elongation. We show, both in vivo and in vitro, that PARP1 binds directly to the Integrator subunit 3 (IntS3), a member of the elongation Integrator complex. The association between the two proteins is mediated via the C-terminal domain of PARP1 to the C-terminal domain of IntS3. Interestingly, the occupancy of IntS3 along two PARP1 target genes mimicked that of PARP1, suggesting a role in its recruitment/assembly of elongation factors. Indeed, the knockdown of PARP1 resulted in differential chromatin association and gene occupancy of IntS3 and other key elongation factors. Most of these PARP1-mediated effects were due to the physical presence of PARP1 rather than its PARylation activity. These studies argue that PARP1 controls the progressive RNAPII elongation complexes. In summary, we present a platform to begin to decipher PARP1's role in recruiting/scaffolding elongation factors along the gene body regions during RNA polymerase II elongation and gene regulation.

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