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

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

ORGANISM(S): Homo sapiens

PROVIDER: GSE186809 | GEO | 2022/03/28

REPOSITORIES: GEO

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ZWC complex-mediated SPT5 phosphorylation suppresses divergent antisense RNA transcription at active gene promoters.

Project description:The human genome encodes large numbers of non-coding RNAs, including divergent antisense transcripts at transcription start sites (TSSs). However, molecular mechanisms by which divergent antisense transcription is regulated have not been detailed. Here, we report a novel ZWC complex composed of ZC3H4, WDR82 and CK2 that suppresses divergent antisense transcription. The ZWC complex preferentially localizes at TSSs of active genes through direct interactions of ZC3H4 and WDR82 subunits with the S5p RNAPII C-terminal domain. ZC3H4 depletion leads to increased divergent antisense transcription, especially at genes that naturally produce divergent antisense transcripts. We further demonstrate that the ZWC complex phosphorylates the previously uncharacterized N-terminal acidic domain of SPT5, a subunit of the transcription-elongation factor DSIF, and that this phosphorylation is responsible for suppressing divergent antisense transcription. Our study provides evidence that the newly identified ZWC-DSIF axis regulates the direction of transcription during the transition from early to productive elongation.

| S-EPMC9023261 | biostudies-literature

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

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

Project description:ZWC Complex-Mediated SPT5 Phosphorylation Suppresses Divergent Antisense RNA Transcription at the Active Gene Promoters

| PRJNA776152 | ENA

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

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

| PRJNA776158 | ENA

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

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

| PRJNA775974 | ENA

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

CTCF blocks antisense transcription initiation at divergent promoters.

Project description:Transcription at most promoters is divergent, initiating at closely spaced oppositely oriented core promoters to produce sense transcripts along with often unstable upstream antisense transcripts (uasTrx). How antisense transcription is regulated and to what extent it is coordinated with sense transcription is not well understood. Here, by combining acute degradation of the multi-functional transcription factor CTCF and nascent transcription measurements, we find that CTCF specifically suppresses antisense but not sense transcription at hundreds of divergent promoters. Primary transcript RNA-FISH shows that CTCF lowers burst fraction but not burst intensity of uasTrx and that co-bursting of sense and antisense transcripts is disfavored. Genome editing, chromatin conformation studies and high-resolution transcript mapping revealed that precisely positioned CTCF directly suppresses the initiation of uasTrx, in a manner independent of its architectural function. In sum, CTCF shapes the transcriptional landscape in part by suppressing upstream antisense transcription.

| S-EPMC10015438 | biostudies-literature

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.

2008-12-01 | GSE12680 | 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

2008-11-06 | GSE13483 | GEO