G+C content of transcribed sequence modulates DSIF-assisted DNA occupancy by RNA polymerase II
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ABSTRACT:
PROVIDER: PRJNA716652 | ENA |
REPOSITORIES: ENA
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Project description:The DSIF complex, which is composed of the Supt4h and Supt5h transcription elongation proteins, clamps RNA polymerase II (RNAPII) onto DNA templates—facilitating polymerase processivity. Lowering of DSIF components can differentially decrease expression of certain neurodegenerative disease-gene alleles containing nucleotide repeat expansions, suggesting that DSIF assists RNAPII progression through these alleles. To identify sequence features that globally affect the actions of DSIF in neuronal cells, we used ultra—deep ChIP-seq analyses together with RNA-seq to investigate and quantify the genome-wide consequences of reducing DSIF on template occupancy and transcription by RNAPII. Our ChIP-seq analysis yielded an average of 378 million reads per sample, facilitating precision in identification of read end-points. The results indicate that DSIF is differentially utilized throughout the human genome by RNAPII in its occupancy of human DNA and that the G+C_composition of the template segment being transcribed determines the extent to which the polymerase relies on DSIF for template occupancy. Additional analysis by us of previously published data obtained. We following knockdown of the Supt5h component of DSIF in murine fibroblasts showed similar effects. We further observed that DSIF reduction resulted in progressively decreased RNAPII occupancy of template during transcript elongation in genes of high G+C content, but had little effect on genes low in G+C content. Our discovery that DSIF dependency varies in different template regions according to G+C content and transcript length suggest a biochemical basis for selective effects of deficiency of DSIF components on genes containing expansions of G+C-rich nucleotide repeats.
2022-07-05 | GSE169465 | GEO
Project description:The DSIF complex, which is composed of the Supt4h and Supt5h transcription elongation proteins, clamps RNA polymerase II (RNAPII) onto DNA templates—facilitating polymerase processivity. Lowering of DSIF components can differentially decrease expression of certain neurodegenerative disease-gene alleles containing nucleotide repeat expansions, suggesting that DSIF assists RNAPII progression through these alleles. To identify sequence features that globally affect the actions of DSIF in neuronal cells, we used ultra—deep ChIP-seq analyses together with RNA-seq to investigate and quantify the genome-wide consequences of reducing DSIF on template occupancy and transcription by RNAPII. Our ChIP-seq analysis yielded an average of 378 million reads per sample, facilitating precision in identification of read end-points. The results indicate that DSIF is differentially utilized throughout the human genome by RNAPII in its occupancy of human DNA and that the G+C_composition of the template segment being transcribed determines the extent to which the polymerase relies on DSIF for template occupancy. Additional analysis by us of previously published data obtained. We following knockdown of the Supt5h component of DSIF in murine fibroblasts showed similar effects. We further observed that DSIF reduction resulted in progressively decreased RNAPII occupancy of template during transcript elongation in genes of high G+C content, but had little effect on genes low in G+C content. Our discovery that DSIF dependency varies in different template regions according to G+C content and transcript length suggest a biochemical basis for selective effects of deficiency of DSIF components on genes containing expansions of G+C-rich nucleotide repeats.
2022-07-05 | GSE169452 | GEO
Project description:G+C content of transcribed sequence modulates DSIF-assisted DNA occupancy by RNA polymerase II [ChIP-seq]
| PRJNA716629 | ENA
Project description:G+C content of transcribed sequence modulates DSIF-assisted DNA occupancy by RNA polymerase II [RNA-seq]
| PRJNA716749 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-07-05 | GSE169466 | GEO
Project description:The DSIF complex comprising the Supt4h and Supt5h transcription elongation proteins clamps RNA polymerase II (RNAPII) onto DNA templates, facilitating polymerase processivity. Lowering DSIF components can differentially decrease expression of alleles containing nucleotide repeat expansions, suggesting that RNAPII transit through repeat expansions is dependent on DSIF functions. To globally identify sequence features that affect dependence of the polymerase on DSIF in human cells, we used ultra-deep ChIP-seq analysis and RNA-seq to investigate and quantify the genome-wide effects of Supt4h loss on template occupancy and transcript production. Our results indicate that RNAPII dependence on Supt4h varies according to G + C content. Effects of DSIF knockdown were prominent during transcription of sequences high in G + C but minimal for sequences low in G + C and were particularly evident for G + C-rich segments of long genes. Reanalysis of previously published ChIP-seq data obtained from mouse cells showed similar effects of template G + C composition on Supt5h actions. Our evidence that DSIF dependency varies globally in different template regions according to template sequence composition suggests that G + C content may have a role in the selectivity of Supt4h knockdown and Supt5h knockdown during transcription of gene alleles containing expansions of G + C-rich repeats.
| S-EPMC9326580 | biostudies-literature
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
Project description:We perform RNA Polymerase II ChIp sequencing on MHV68 infected MC57G B6 mouse fibroblasts alongside a MHV68 mutant (R443I) that is deficient for RNA decay. We profile the occupancy of Pol II on host and viral genes at 24h post infection.We find that host genes have less Pol II occpancy genome wide, while viral genes remain robustly transcribed irrespective of RNA decay.
2019-06-12 | GSE132574 | GEO
Project description:Control of gene expression is one of the most complex yet continuous physiological processes impacting cellular homeostasis. RNA polymerase II (Pol II) transcription is tightly regulated at promoter-proximal regions by intricate dynamic processes including Pol II pausing, release into elongation and premature termination. Pol II pausing is a phenomenon where Pol II complex pauses within 30-60 nucleotides after initiating the transcription. Negative elongation factor (NELF) and DRB sensitivity inducing factor (DSIF) contribute in the establishment of Pol II pausing, and positive transcription elongation factor b releases (P-TEFb) paused complex after phosphorylating DSIF that leads to dissociation of NELF. Pol II pausing is observed in most expressed genes across the metazoan. The precise role of Pol II pausing is not well understood; however, it's required for integration of signals for gene regulation. In the present study, we investigated the role of phosphatase and tensin homolog (PTEN) in genome-wide transcriptional regulation using PTEN overexpression and PTEN knock-down models. Here we identify that PTEN alters the expression of hundreds of genes, and its restoration establishes genome-wide Pol II promoter-proximal pausing in PTEN null cells. Furthermore, PTEN re-distributes Pol II occupancy across the genome and possibly impacts Pol II pause duration, release and elongation rate in order to enable precise gene regulation at the genome-wide scale. Our observations demonstrate an imperative role of PTEN in global transcriptional regulation that will provide a new direction to understand PTEN-associated pathologies and its management.
| S-EPMC6735678 | biostudies-literature
Project description:Improve the reliability of the phosphosite occupancy determined by the third method by comparison of the ratio of absolute occupancy and relative occupancy from HCC samples. An outlier score was introduced to evaluate the deviation between ratio of absolute occupancy and relative occupancy and further to balance the confidence interval and deviation instead of set a fixed threshold.
2020-08-06 | PXD019045 | Pride