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Genome wide profiling of RNA Polymerase II upon knock-down or overexpression of RECQL5

ABSTRACT: RECQL5 globally effects the distribution of RNA Polymerase II on genes in a dose dependent manner. Knock-down of RECQL5 reduces RNA Polymerase II density in the gene body, while increasing density on TSS and TTS. Overexpression shows exactly the opposite effect. We postulate that RECQL5 acts as a regulator of the elongation rate, more specifically, that the knock-down increases elongation rate while the overexpression decreases it.

ORGANISM(S): Homo sapiens

PROVIDER: GSE49008 | GEO | 2014/06/09

SECONDARY ACCESSION(S): PRJNA212573

REPOSITORIES: GEO

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Genome wide profiling of RNA Polymerase II upon knock-down or overexpression of RECQL5

Project description:RECQL5 globally effects the distribution of RNA Polymerase II on genes in a dose dependent manner. Knock-down of RECQL5 reduces RNA Polymerase II density in the gene body, while increasing density on TSS and TTS. Overexpression shows exactly the opposite effect. We postulate that RECQL5 acts as a regulator of the elongation rate, more specifically, that the knock-down increases elongation rate while the overexpression decreases it. RNA Polymerase II ChIP-Seq upon knock-down of RECQL5 with either of two specific shRNAs or a CTRL shRNA, and upon Doxycycline induced overexpression of RECQL5 .

2014-06-09 | E-GEOD-49008 | biostudies-arrayexpress

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Signaling Pathways Deferentially Affect RNA Polymerase II Initiation, Pausing, and Elongation in Human Cells: Estrogen dependent signaling in MCF-7 cells

Project description:We used Global Run-on and Sequencing (GRO-seq) to measure the rate of transcription elongation by RNA polymerase II (Pol II) following gene activation. We observed that Pol II elongation rates can vary as much as 4-fold at different genomic loci and in response to two distinct cellular signaling pathways (i.e., estrogen and TNFα). Elongation rates are slowest near the promoter and increase during the first ~15 kb transcribed into the gene body. Gene body elongation rates correlate with the density of Pol II, consequently resulting in systematically higher rates of transcript production at genes with higher Pol II density. By monitoring Pol II dynamics following short inductions, we found that E2 stimulates gene expression by increasing Pol II initiation, whereas TNFα stimulates the release of Pol II from promoter proximal pause sites. Collectively, our results identify previously uncharacterized variation in the rate of Pol II elongation and highlight elongation as an important, variable, and regulated rate limiting step in the transcription cycle.

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Signaling Pathways Deferentially Affect RNA Polymerase II Initiation, Pausing, and Elongation in Human Cells: TNF-alpha dependent signaling in AC16 cells

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Signaling Pathways Deferentially Affect RNA Polymerase II Initiation, Pausing, and Elongation in Human Cells: TNF-alpha dependent signaling in AC16 cells

Project description:We used Global Run-on and Sequencing (GRO-seq) to measure the rate of transcription elongation by RNA polymerase II (Pol II) following gene activation. We observed that Pol II elongation rates can vary as much as 4-fold at different genomic loci and in response to two distinct cellular signaling pathways (i.e., estrogen and TNFM-NM-1). Elongation rates are slowest near the promoter and increase during the first ~15 kb transcribed into the gene body. Gene body elongation rates correlate with the density of Pol II, consequently resulting in systematically higher rates of transcript production at genes with higher Pol II density. By monitoring Pol II dynamics following short inductions, we found that E2 stimulates gene expression by increasing Pol II initiation, whereas TNFM-NM-1 stimulates the release of Pol II from promoter proximal pause sites. Collectively, our results identify previously uncharacterized variation in the rate of Pol II elongation and highlight elongation as an important, variable, and regulated rate limiting step in the transcription cycle. Using GRO-seq over a time course (0, 10, 25, and 40 min) of estrogen signaling in ER-alpha positive MCF-7 human breast cancer cells.

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Project description:Production of mRNA depends critically on the rate of RNA polymerase II (Pol II) elongation. To dissect Pol II dynamics in mouse ES cells, we inhibited Pol II transcription at either initiation or promoter-proximal pause escape with Triptolide or Flavopiridol, and tracked Pol II kinetically using GRO-seq. Both inhibitors block transcription of more than 95% of genes, showing that pause escape, like initiation, is a ubiquitous and crucial step within the transcription cycle. Moreover, paused Pol II is relatively stable, as evidenced from half-life measurements at ~3200 genes. Finally, tracking the progression of Pol II after drug treatment establishes Pol II elongation rates at over 1,000 genes. Notably, Pol II accelerates dramatically while transcribing through genes, but slows at exons. Furthermore, intergenic variance in elongation rates is substantial, and is influenced by a positive effect of H3K79me2 and negative effects of exon density and CG content within genes.

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Project description:RNA polymerase II elongation rate controls gene expression by alternative polyadenylation

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