The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA630757 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11714163.fastq.gz | Fastqsanger.gz | |||
| SRR11714164.fastq.gz | Fastqsanger.gz | |||
| SRR11714165.fastq.gz | Fastqsanger.gz | |||
| SRR11714166.fastq.gz | Fastqsanger.gz | |||
| SRR11714167.fastq.gz | Fastqsanger.gz |
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Project description:The RNA polymerase II (RNAPII) associated factor 1 complex (Paf1C) plays critical roles in modulating the release of paused RNAPII into productive elongation. However, regulation of Paf1C-mediated promoter-proximal pausing is complex and context dependent. In fact, in cancer cell lines opposing models of Paf1Cs’ role in RNAPII pause-release control have been proposed. Here we show that the Paf1C positively regulates RNAPII pause-release at both protein-coding genes and at enhancers in mouse embryonic stem cells (mESC). Our analyses reveal extensive Paf1C binding at mESC enhancers, in particular at super enhancers. Importantly, Paf1C occupancy correlates with the strength of enhancer activity. Depletion of Paf1C attenuates the expression of genes regulated by targeted enhancers and affects RNAPII Ser2 phosphorylation at the binding sites, suggesting that mESC self-renewal depends on Paf1C-mediated positive regulation of pluripotency enhancers.
2020-12-25 | GSE149999 | GEO
Project description:The RNA polymerase II (RNAPII) associated factor 1 complex (Paf1C) plays critical roles in modulating the release of paused RNAPII into productive elongation. However, regulation of Paf1C-mediated promoter-proximal pausing is complex and context dependent. In fact, in cancer cell lines, opposing models of Paf1Cs' role in RNAPII pause-release control have been proposed. Here, we show that the Paf1C positively regulates enhancer activity in mouse embryonic stem cells. In particular, our analyses reveal extensive Paf1C occupancy and function at super enhancers. Importantly, Paf1C occupancy correlates with the strength of enhancer activity, improving the predictive power to classify enhancers in genomic sequences. Depletion of Paf1C attenuates the expression of genes regulated by targeted enhancers and affects RNAPII Ser2 phosphorylation at the binding sites, suggesting that Paf1C-mediated positive regulation of pluripotency enhancers is crucial to maintain mouse embryonic stem cell self-renewal.
| S-EPMC7772781 | biostudies-literature
Project description:Phf5a regulates transcription elongation in mouse embryonic stem cells (ESCs), through regulation of the Paf1 complex. In this study we assayed for genome-wide localization of Paf1, Leo1 and Cdc73 subunits of the Paf1 complex in mouse ESCs under conditions of shControl and shPhf5a knockdown. These results revealed that downregualtion of Phf5a results in the significant decrease of Paf1 complex binding to its targets in ESCs.
2016-08-31 | GSE73445 | GEO
Project description:To identify the direct targets of the Paf1/RNA polymerase II complex we compared expression profiles of isogenic wild type and paf1 and ctr9 mutant strains. We also created a Tet-regulated form of Paf1 and monitored expression patterns after shut off of Paf1. Samples were isolated at one hour intervals from 1 to 8 hours after shut off. Experiment Overall Design: Transcripts were compared on Affymetrix microarrays using standard protocols.
2007-09-19 | E-GEOD-3200 | biostudies-arrayexpress
Project description:Gene expression in metazoans is regulated by RNA Polymerase II (Pol II) promoter-proximal pausing and its release. Previously, we identified that Pol II-associated factor 1 (PAF1) modulates the release of paused Pol II into productive elongation. Here, we find that PAF1 occupies transcriptional enhancers and restrains hyperactivation of a subset of these enhancers. Enhancer activation as the result of Paf1 loss releases Pol II from paused promoters of nearby PAF1 target genes. Knockout of PAF1-regulated enhancers attenuates the release of paused Pol II on PAF1 target genes without major interference in the establishment of pausing at their cognate promoters. Thus, a subset of enhancers can primarily modulate gene expression by controlling the release of paused Pol II in a PAF1-dependent manner.
2017-09-01 | GSE97527 | GEO
Project description:In this study, we found that the ARF tumor suppressor directly binds the PAF1 subunit to block the assembly of PAF1 complex (PAF1c) and its interaction with RNAPII, thereby dampening PAF1c-dependent transcription in vitro and in cells. To investigate whether ARF regulates RNAPII and PAF1c occupancy at putative target genes identified through RNA-seq, we performed ChIP-seq (RNAPII, PAF1, and CTR9) in ARF (shARF) vs. control (shNT) knockdown MEFs. Our data show that loss of ARF increases RNAPII, PAF1, and CTR9 occupancy on upregulated genes, consistent with ARF-mediated gene-specific repression. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNA polymerase subunit RPB3 and PAF1 complex subunits PAF1 and CTR9 in mouse embryonic fibroblasts.
2024-10-10 | GSE217765 | GEO
Project description:Small RNA molecules are well known for silencing gene expression post-transcriptionally, but they are also implicated in epigenetic regulation across kingdoms. However, the mechanisms of epigenetic gene silencing by small RNAs are mostly unknown. In addition, stably silencing genes de novo using synthetic small RNAs to trigger locus-independent heterochromatin formation is impossible. Using fission yeast, we show that RNA-directed heterochromatin formation is negatively controlled by the highly conserved RNA polymerase-associated factor 1 (Paf1) complex. Temporary expression of a synthetic hairpin RNA in Paf1 mutants triggers stable heterochromatin formation at homologous loci, effectively silencing genes in trans. This repressed state is propagated over many generations by continual production of secondary siRNAs, independently of the synthetic hairpin RNA. Our work uncovers a novel mechanism for small RNA-mediated epigenome regulation and highlights fundamental roles for the Paf1 complex and the RNA interference machinery in building epigenetic memory.
2015-03-25 | GSE59170 | GEO
Project description:Small RNA molecules are well known for silencing gene expression post-transcriptionally, but they are also implicated in epigenetic regulation across kingdoms. However, the mechanisms of epigenetic gene silencing by small RNAs are mostly unknown. In addition, stably silencing genes de novo using synthetic small RNAs to trigger locus-independent heterochromatin formation is impossible. Using fission yeast, we show that RNA-directed heterochromatin formation is negatively controlled by the highly conserved RNA polymerase-associated factor 1 (Paf1) complex. Temporary expression of a synthetic hairpin RNA in Paf1 mutants triggers stable heterochromatin formation at homologous loci, effectively silencing genes in trans. This repressed state is propagated over many generations by continual production of secondary siRNAs, independently of the synthetic hairpin RNA. Our work uncovers a novel mechanism for small RNA-mediated epigenome regulation and highlights fundamental roles for the Paf1 complex and the RNA interference machinery in building epigenetic memory.
2015-03-25 | GSE59169 | GEO
Project description:Chromatin places fundamental physical constraints on transcription (Gamarra and Narlikar, 2021). The PAF1 complex (PAF1C), a hexamer of PAF1, LEO1, CTR9, SKI8, CDC73 and RTF1, plays a critical role in transcription with incompletely understood mechanisms. During transcriptional elongation, PAF1C is one of the positive elongation factors in complex with RNA polymerase II (Pol II) to facilitate elongation through chromatin (Vos et al., 2018), but it is unclear yet if negative elongation factors are needed concurrently to restrain elongation. Here we show that besides decreasing elongation rate, LEO1 knockout in human K562 cells increases transcriptional readthrough and cellular level of C-terminal domain (CTD) phosphorylated Pol II while increases and decreases transcriptional output of several hundred genes, respectively. Mechanistic analyses taking proteomic, functional genomic and biochemical approaches discovered that PAF1C regulates transcriptional termination in part through recruiting PNUTS-PP1γ complex and facilitates Pol II transcriptional re-initiation through recruiting TOX4-PP1α complex. Moreover, Paf1 conditional knockout in mice severely blocks T cell development, increases cellular level of CTD phosphorylated Pol II, mainly decreases Pol II occupancy and transcriptional output in double positive T cells, and importantly, the regulation of re-initiation by PAF1C through TOX4-PP1α complex is conserved between mouse and human. Our results also suggest that PNUTS-PP1γ and TOX4-PP1α bind PAF1C to restrain Pol II elongation through chromatin. These findings not only establish PAF1C as a critical regulator of transcriptional termination and re-initiation besides elongation but also advanced current understanding of elongation.
2024-11-06 | GSE188417 | GEO
Project description:To identify the direct targets of the Paf1/RNA polymerase II complex we compared expression profiles of isogenic wild type and paf1 and ctr9 mutant strains. We also created a Tet-regulated form of Paf1 and monitored expression patterns after shut off of Paf1. Samples were isolated at one hour intervals from 1 to 8 hours after shut off. Keywords: single channel nucleotide
2005-08-26 | GSE3200 | GEO