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Divergent transcription from active promoters

ABSTRACT: Here we describe a novel class of short RNAs and high-resolution ChIP-Seq data that together indicate widespread divergent transcription at mammalian promoters and suggest the existence of novel regulatory mechanisms concerning both initiation and elongation by RNA polymerase II.

ORGANISM(S): Mus musculus

PROVIDER: GSE12680 | GEO | 2008/12/01

SECONDARY ACCESSION(S): PRJNA112677

REPOSITORIES: GEO

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Divergent transcription from active promoters

Project description:Here we describe a novel class of short RNAs and high-resolution ChIP-Seq data that together indicate widespread divergent transcription at mammalian promoters and suggest the existence of novel regulatory mechanisms concerning both initiation and elongation by RNA polymerase II. ChIP-seq in murine embryonic stem cells for RNA polymerase II

2008-12-01 | E-GEOD-12680 | biostudies-arrayexpress

Divergent transcription from active promoters

Project description:Here we describe a novel class of short RNAs that indicate widespread divergent transcription at mammalian promoters

2008-11-06 | GSE13483 | GEO

Divergent transcription from active promoters

Project description:Here we describe a novel class of short RNAs that indicate widespread divergent transcription at mammalian promoters Small RNA cloning and deep sequencing from human embryonic stem cells, derived neural progenitors and neurons

2008-11-06 | E-GEOD-13483 | biostudies-arrayexpress

ZWC Complex-Mediated SPT5 Phosphorylation Suppresses Divergent Antisense RNA Transcription at the Active Gene Promoters [RNA-Seq]

Project description:Purpose: The goals of this study are to understand the mechanistic roles of newly identified ZWC chromatin complex on the regulation of transcriptional process in actively transcribed genes. The novel ZWC complex is composed of ZC3H4, WDR82, and casein kinase II (CK2) subunits. Methods: Three biological replicates of RNA-seq data were generated after HEK293 cells were treated with control or ZC3H4 siRNAs. The RNA-Seq libraries were generated from 200 ng of total RNA using TruSeq Stranded Total RNA Library Prep kit (Illumina) according to the manufacturer's protocol. Results: The ZWC complex preferentially localizes at TSSs of active genes through the direct interactions of ZC3H4 and WDR82 subunits with S5p RNAPII CTD. ZC3H4 depletion leads to increased divergent antisense transcription. Conclusion: Our study provides evidence that the newly identified ZWC-DSIF axis regulates the direction of transcription during the transition from early to productive elongation

2022-03-28 | GSE186808 | GEO

ZWC Complex-Mediated SPT5 Phosphorylation Suppresses Divergent Antisense RNA Transcription at the Active Gene Promoters [ChIP-Seq]

Project description:Purpose: The goals of this study are to understand the mechanistic roles of newly identified ZWC chromatin complex on the regulation of transcriptional process in actively transcribed genes. The novel ZWC complex is composed of ZC3H4, WDR82, and casein kinase II (CK2) subunits. Methods: Two biological replicates of ChIP-seq data for ZC3H4, WDR82, CK2, and SPT5 were generated from HEK293 cells. And one replicate of ChIP-seq data for RNAPII, H3K4me3, H3K27me3, and H3K36me3 was generated in HEK293 cells. Two biological replicates of ChIP-seq data were generated for RNAPII, S5p RNAPII, S2p RNAPII, SPT5, H3K4me3, H3K36me3, H3K27me3 after HEK293 cells were treated with control or ZC3H4 siRNAs. Results: The ZWC complex preferentially localizes at TSSs of active genes through the direct interactions of ZC3H4 and WDR82 subunits with S5p RNAPII CTD. ZC3H4 depletion leads to increased divergent antisense transcription. Conclusion: Our study provides evidence that the newly identified ZWC-DSIF axis regulates the direction of transcription during the transition from early to productive elongation

2022-03-28 | GSE186758 | GEO

Divergent transcription from active promoters.

Project description:Transcription initiation by RNA polymerase II (RNAPII) is thought to occur unidirectionally from most genes. Here, we present evidence of widespread divergent transcription at protein-encoding gene promoters. Transcription start site-associated RNAs (TSSa-RNAs) nonrandomly flank active promoters, with peaks of antisense and sense short RNAs at 250 nucleotides upstream and 50 nucleotides downstream of TSSs, respectively. Northern analysis shows that TSSa-RNAs are subsets of an RNA population 20 to 90 nucleotides in length. Promoter-associated RNAPII and H3K4-trimethylated histones, transcription initiation hallmarks, colocalize at sense and antisense TSSa-RNA positions; however, H3K79-dimethylated histones, characteristic of elongating RNAPII, are only present downstream of TSSs. These results suggest that divergent transcription over short distances is common for active promoters and may help promoter regions maintain a state poised for subsequent regulation.

| S-EPMC2692996 | biostudies-literature

Aclarubicin stimulates RNA polymerase II elongation at closely spaced divergent promoters

Project description:Aclarubicin stimulates RNA polymerase II elongation at closely spaced divergent promoters

| PRJNA913597 | ENA

Aclarubicin stimulates RNA polymerase II elongation at closely spaced divergent promoters

Project description:Anthracyclines are a class of widely prescribed anti-cancer drugs that disrupt chromatin by intercalating into DNA and enhancing nucleosome turnover. To understand the molecular consequences of anthracycline-mediated chromatin disruption, we utilized CUT&Tag to profile RNA polymerase II during anthracycline treatment in Drosophila cells. We observed that treatment with the anthracycline aclarubicin leads to elevated levels of elongating RNA polymerase II and changes in chromatin accessibility. We found that promoter proximity and orientation impacts chromatin changes during aclarubicin treatment, as closely spaced divergent promoter pairs show greater chromatin changes when compared to codirectionally-oriented tandem promoters. We also found that aclarubicin treatment changes the distribution of non-canonical DNA G-quadruplex structures both at promoters and at G-rich pericentromeric repeats. Our work suggests that aclarubicin's anti-cancer activity is driven by the effects of nucleosome disruption on RNA polymerase II, chromatin accessibility and DNA structures.

2023-05-04 | GSE221252 | GEO

Hda1C restricts burst frequency to limit divergent non-coding transcription

Project description:We used Native Elongation Transcript sequencing (NET-seq) to investigate the genome-wide effect of the Hda1 histone deacetylase complex (Hda1C) on the repression of divergent non-coding (DNC) transcription at bidirectional promoters in yeast S.cerevisiae.

2021-08-02 | GSE167499 | GEO

A high-resolution map of active promoters in the human genome

Project description:Our ability to understand the control logic embedded in the human genome is limited by a lack of accurate information of the promoter sequences for most genes. Promoters are a unique class of control sequences, serving as the binding sites for both sequence-specific factors and the general transcription machinery during transcription initiation. In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex throughout the non-repeat sequences of the human genome in primary fibroblast cells. The resulting map defines 10,571 active promoters corresponding to 6,763 known genes and at least 1,199 un-annotated transcriptional units. The map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome. Further examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell. Our results provide a global view of the functional relationship among the transcriptional machinery, chromatin structure, and gene expression in human cells. Keywords = GALA Keywords = gene expression Keywords = nimblegen Keywords = promoter profile Keywords = LICR renlab Keywords: other

2010-07-01 | E-GEOD-2672 | biostudies-arrayexpress

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