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Oxidative stress elicits a rapid and global RNA polymerase II transcriptional response in human cells

ABSTRACT: In GSE93931, we used ChIP-Seq to show that hydrogen peroxide causes rapid accumulation of Pol II at promoters and enhancers. Over time, a fraction of accumulated Pol II loses NELF and creeps downstream. In GSE100740, we also compared nuclear walk-on results with PRO-Seq, both of which were performed using nuclei from DMSO- and flavopiridol-treated cells. This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE100742 | GEO | 2017/08/07

SECONDARY ACCESSION(S): PRJNA392903

REPOSITORIES: GEO

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Oxidative stress elicits a rapid and global RNA polymerase II transcriptional response in human cells [PRO-Seq]

Project description:We compared nuclear walk-on results with PRO-Seq, both of which were performed using nuclei from DMSO- and flavopiridol-treated cells. In GSE93931, we also used ChIP-Seq to show that hydrogen peroxide causes rapid accumulation of Pol II at promoters and enhancers. Over time, a fraction of accumulated Pol II loses NELF and creeps downstream.

2017-08-07 | GSE100740 | GEO

Oxidative stress elicits a rapid and global RNA polymerase II transcriptional response in human cells [ChIP-Seq]

Project description:Using ChIP-Seq, we show that hydrogen peroxide causes rapid accumulation of Pol II at promoters and enhancers. Over time, a fraction of accumulated Pol II loses NELF and creeps downstream. In GSE100740, we also compared nuclear walk-on results with PRO-Seq, both of which were performed using nuclei from DMSO- and flavopiridol-treated cells.

2017-08-07 | GSE93931 | GEO

Postrecruitment Regulation of RNA Pol II Directs Rapid Signaling Responses at the Promoters of Estrogen Target Genes

Project description:Under current models for signal-dependent transcription in eukaryotes, DNA-binding activator proteins regulate the recruitment of RNA polymerase II (Pol II) to a set of target promoters. Yet, recent studies, as well as our results herein, show that Pol II is widely distributed (i.e., "preloaded") at the promoters of many genes prior to specific signaling events. How Pol II recruitment and Pol II preloading fit within a unified model of gene regulation is unclear. In addition, the mechanisms through which cellular signals activate preloaded Pol II across mammalian genomes remain largely unknown. Here we show that the predominant genomic outcome of estrogen signaling is the post-recruitment regulation of Pol II activity through phosphorylation, rather than recruitment of Pol II. Furthermore, we show that negative elongation factor (NELF) binds to estrogen target promoters in conjunction with preloaded Pol II and represses gene expression until the appropriate signal is received. Finally, our studies reveal that the estrogen-dependent activation of preloaded Pol II facilitates rapid transcriptional and post-transcriptional responses which play important physiological roles in regulating estrogen signaling itself. Our results reveal a broad use of post-recruitment Pol II regulation by the estrogen signaling pathway, a mode of regulation that is likely to apply to a wide variety of signal-regulated pathways. ChIP-chip analysis for RNA Pol II, Ser5 phosphorylated RNA Pol II and NELF-A in MCF7 breast cancer cells.

2010-05-14 | E-GEOD-13051 | biostudies-arrayexpress

Genome-wide map of RNA polymerase II, NELF, and DSIF in HeLa cells

Project description:Most metazoan promoters have RNA polymerase II (Pol II) paused slightly downstream of the transcription start site by NELF and DSIF. This pausing keeps these promoters available for rapid induction by P-TEFb, whose activity causes NELF to dissociate and Pol II and DSIF to elongate on the gene. ChIP-Seq data was generated for Pol II, NELF, and DSIF in HeLa cells and used to look at pausing downstream of unannotated promoters. 3x ChIP-Seq (Pol II, NELF, DSIF) in HeLa cells

2014-02-01 | E-GEOD-53008 | biostudies-arrayexpress

Regulation of Mammalian Cell Growth and Survival By an RNA Polymerase II-Pausing Factor (ChIP-seq)

Project description:Many mammalian genes are occupied by paused RNA polymerase II (pol II) at promoter-proximal regions on both sides of transcription start sites (TSSs). However, the consequences of pol II pausing on gene expression and cell biology are not fully understood. Here we report that genetic ablation of the b subunit of mouse negative elongation factor (Nelf-b), a key pol II-pausing factor, results in slower progression at multiple cell cycle stages and increased apoptosis. Consistently, a whole-genome analysis indicates that growth and cell death-related genes are highly enriched among the direct target genes of Nelf-b. In particular, Nelf-b deletion increases pol II density in the promoter-distal region of stress response genes and their overall expression levels in the absence of any external stress signals. In addition, our work also reveals a previously unappreciated role of Nelf-b role in curbing TSS-upstream transcription of many mammalian genes. We suggest that Nelf-mediated pol II pausing balances the cellular needs for growth/survival and stress response by preventing excessive basal transcription of stress-induced genes. Examination of Nelf-b bindings sites on chromosomes in mouse embryonic fibroblasts

2011-08-17 | E-GEOD-24113 | biostudies-arrayexpress

Genome-wide map of RNA polymerase II, NELF, and DSIF in HeLa cells

2014-02-01 | GSE53008 | GEO

Regulation of Mammalian Cell Growth and Survival By an RNA Polymerase II-Pausing Factor (Gene expression)

Project description:Many mammalian genes are occupied by paused RNA polymerase II (pol II) at promoter-proximal regions on both sides of transcription start sites (TSSs). However, the consequences of pol II pausing on gene expression and cell biology are not fully understood. Here we report that genetic ablation of the b subunit of mouse negative elongation factor (Nelf-b), a key pol II-pausing factor, results in slower progression at multiple cell cycle stages and increased apoptosis. Consistently, a whole-genome analysis indicates that growth and cell death-related genes are highly enriched among the direct target genes of Nelf-b. In particular, Nelf-b deletion increases pol II density in the promoter-distal region of stress response genes and their overall expression levels in the absence of any external stress signals. In addition, our work also reveals a previously unappreciated role of Nelf-b role in curbing TSS-upstream transcription of many mammalian genes. We suggest that Nelf-mediated pol II pausing balances the cellular needs for growth/survival and stress response by preventing excessive basal transcription of stress-induced genes. Immortalized mouse embryonic fibroblasts derived from a Nelf-b flox/- embryo were infected with control or Cre-epxressing retrovirus. Gene expression profile of control and knockout MEF at 7 days after virus infection were compared by using Illumina's mouse whole-genome gene expression BeadChIPs. There are two replicates for both control and knockout MEF samples.

2011-08-16 | E-GEOD-24114 | biostudies-arrayexpress

SPT6 functions in transcriptional pause/release via PAF1C recruitment

Project description:In vitro studies identified various factors including P-TEFb, SEC, SPT6, PAF1, DSIF, and NELF functioning at different stages of transcription elongation driven by RNA polymerase II (RNA Pol II). What remains unclear is how these factors cooperatively regulate pause/release and productive elongation in the context of living cells. Using an acute 5 protein-depletion approach, prominent release and a subsequent increase in mature transcripts, whereas long genes fail to yield mature transcripts due to a loss of processivity. Mechanistically, loss of SPT6 results in loss of PAF1 complex (PAF1C) from RNA Pol II, leading to NELF-bound RNA Pol II release into the gene bodies. Furthermore, SPT6 and/or PAF1 depletion impairs heat shock-induced pausing, pointing to a role for SPT6 in regulating RNA Pol II pause/release through the recruitment of PAF1C during the early elongation.

2022-08-09 | PXD033771 | Pride

Essential Signaling Function of Cytoplasmic NELFB Independent of RNA Polymerase II Pausing [ChIP-seq]

Project description:Biochemical studies have established that the four-subunit negative elongation factor (NELF) complex mediates RNA polymerase II (Pol II) pausing at promoter proximal regions. Genetic ablation of individual NELF subunits destabilizes the entire NELF complex and causes lethality of cultured cells, leading to the prevailing concept that NELF-mediated Pol II pausing is essential for cell survival. Using separation-of-function mutations, we show here that NELFB’s effects on cell proliferation can be uncoupled from its function in Pol II pausing. NELFB mutants localized in the cytoplasm and incapacitated in the NELF complex assembly still retain their ability to support cell proliferation and at least part of NELFB-dependent transcriptome. Furthermore, we demonstrate that cytoplasmic NELFB physically and functionally interacts with multiple pro-survival signaling kinases, most notably PI3K/AKT. Enforced activation of PI3K/AKT-related kinases largely rescues deficiency of NELFB-depleted cells in proliferation, but not Pol II pausing. Together, these data revise the current understanding of the growth impact of Pol II pausing and underscore multiplicity of the biological function of individual NELF subunits.

2023-06-30 | GSE205504 | GEO

Essential Signaling Function of Cytoplasmic NELFB Independent of RNA Polymerase II Pausing

2023-06-30 | GSE205388 | GEO