RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription
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ABSTRACT:
PROVIDER: PRJNA806677 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18010300_1.fastq.gz | Fastqsanger.gz | |||
| SRR18010300_2.fastq.gz | Fastqsanger.gz | |||
| SRR18010301_1.fastq.gz | Fastqsanger.gz | |||
| SRR18010301_2.fastq.gz | Fastqsanger.gz | |||
| SRR18010302_1.fastq.gz | Fastqsanger.gz |
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Project description:RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription
| PRJNA805293 | ENA
Project description:PRO-seq experiment of Nelfb deg mESC in serum/LIF or during pluripotency transitions, with or without dTAG-13.
2022-02-16 | GSE196653 | GEO
Project description:Promoter-proximal RNA Pol II pausing is a critical step in transcriptional control. Pol II pausing has been predominantly studied in tissue culture systems. While Pol II pausing has been shown to be required for mammalian development, the phenotypic and mechanistic details of this requirement are unknown. Here, we found that loss of Pol II pausing stalls pluripotent state transitions within the epiblast of the early mouse embryo. Using Nelfb -/- mice and a NELFB degron mouse pluripotent stem cell model, we show that embryonic stem cells (ESCs) representing the naïve state of pluripotency successfully initiate a transition program but fail to balance levels of induced and repressed genes and enhancers in the absence of NELF. We found an increase in chromatin-associated NELF during transition from the naïve to later pluripotent states. Overall, our work defines the acute and long-term molecular consequences of NELF loss and reveals a role for Pol II pausing in the pluripotency continuum as a modulator of cell state transitions.
| S-EPMC9480856 | biostudies-literature
Project description:ChIP-seq experiments of NELFB (HA), NELFE, and Spt5 in mESCs under serum/LIF conditions. The experiments where performed with and without dTAG degradation of NELFB
2022-02-28 | GSE196543 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE31485: CTCF promotes RNA pol II pausing and links DNA methylation to alternative splicing [ChIP-Seq] GSE31486: CTCF promotes RNA pol II pausing and links DNA methylation to alternative splicing [RNA-Seq] Refer to individual Series
2011-10-05 | E-GEOD-31278 | biostudies-arrayexpress
Project description:Fluctuations in nutrient availability profoundly impact gene expression. Previous work revealed post-recruitment regulation of RNA Polymerase II (Pol II) during starvation and recovery in Caenorhabitis elegans, suggesting promoter-proximal pausing promotes rapid response to feeding. To test this hypothesis, we measured Pol II elongation genome-wide by two complementary approaches and analyzed elongation in conjunction with Pol II binding and expression. We confirmed bona fide pausing during starvation and also discovered Pol II docking. Pausing occurs at active stress-response genes that become down-regulated in response to feeding. In contrast M-bM-^@M-^\dockedM-bM-^@M-^] Pol II accumulates without initiating upstream of inactive growth genes that become rapidly up-regulated upon feeding. Beyond differences in function and expression, these two sets of genes have different core promoter motifs, suggesting alternative transcriptional machinery. Our work suggests that growth and stress genes are both regulated post-recruitment during starvation, but at initiation and elongation, respectively, coordinating gene expression with nutrient availability. We sequenced short, capped RNA (scRNA-seq) from N2 starved L1 C. elegans as well as a TFIIS mutant (RB2083). We also prepared scRNA-seq libraries from L1 larvae using one, two, or three of the enymes used to prepare the scRNA sequencing libraries as well as scRNA-seq libraries from Drosophila S2 cells using one or two of the enzymes. We further sequenced the 5' end of mRNA in starved C. elegans L1 larvae using the same enzymes as scRNA-seq.
2014-02-01 | E-GEOD-40161 | biostudies-arrayexpress
Project description:Fluctuations in nutrient availability profoundly impact gene expression. Previous work revealed post-recruitment regulation of RNA Polymerase II (Pol II) during starvation and recovery in Caenorhabitis elegans, suggesting promoter-proximal pausing promotes rapid response to feeding. To test this hypothesis, we measured Pol II elongation genome-wide by two complementary approaches and analyzed elongation in conjunction with Pol II binding and expression. We confirmed bona fide pausing during starvation and also discovered Pol II docking. Pausing occurs at active stress-response genes that become down-regulated in response to feeding. In contrast “docked” Pol II accumulates without initiating upstream of inactive growth genes that become rapidly up-regulated upon feeding. Beyond differences in function and expression, these two sets of genes have different core promoter motifs, suggesting alternative transcriptional machinery. Our work suggests that growth and stress genes are both regulated post-recruitment during starvation, but at initiation and elongation, respectively, coordinating gene expression with nutrient availability.
2014-02-01 | GSE40161 | GEO
Project description:We prepared and sequenced Start-seq libraries from rat (Rattus norgevicus) primary neural progenitor cells. Over 48 million uniquely mappable reads from two independent biological replicates allowed us to define the TSSs of 7,365 known genes in the rn6 genome, reannotating 2,503 TSSs by more than 5 base pairs, characterize promoter-associated antisense transcription, and profile Pol II pausing. By combining TSS data with polyA-selected RNA sequencing, we also identified thousands of potential new genes producing stable RNA as well as non-genic transcripts representing possible regulatory elements. CONCLUSIONS: Our study has produced the first Start-seq dataset for the rat. Apart from profiling transcription initiation, our data reaffirm the prevalence of Pol II pausing across the rat genome and indicate conservation of pausing mechanisms across metazoan genomes. We suggest that pausing location, at least in mammals, is constrained by a distance from initiation of transcription, whether it occurs at or outside of a gene promoter. Abundant antisense transcription initiation around protein coding genes indicates that Pol II recruited to the vicinity of a promoter is distributed to available start sites of transcription at either DNA strand. Transcriptome profiling of neural progenitors presented here will facilitate further studies of other rat cell types as well as other organisms.
2019-06-20 | GSE130338 | GEO
Project description:RNA polymerase II (pol II) transcribes all protein-coding and many non-coding RNAs in the human genome. Pol II transcription initiation is governed by the Pre-Initiation Complex (PIC), which contains TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, pol II, and Mediator. After initiation, pol II enzymes typically pause after transcribing less than 100 bases, and paused polymerases represent a common regulatory intermediate. Accordingly, paused pol II has been implicated in enhancer function, development and homeostasis, and diseases ranging from cancer to viral pathogenesis. Precisely how pol II promoter-proximal pausing is enforced and regulated remains unclear; however, protein complexes such as NELF and DSIF increase pausing whereas the activity of CDK9 (P-TEFb complex) correlates with pause release. To address specific mechanistic questions about pol II pausing and its regulation, we reconstituted human pol II promoter-proximal pausing in vitro, entirely with purified factors (no extracts). As expected, NELF and DSIF increased pol II pausing in vitro, whereas P-TEFb promoted pause release. Unexpectedly, the PIC alone was sufficient to reconstitute pol II pausing, suggesting that pausing is an inherent property of the PIC. In agreement, pol II pausing was lost upon replacement of the TFIID complex with TATA-binding protein (TBP); moreover, pausing was dependent upon TFIID subunits TAF1 and TAF2. TAF1/2 bind genomic DNA downstream of the pol II initiation site, invoking a “complex interaction” model for pausing. Consistent with this model, PRO-Seq experiments revealed increased transcription upon acute depletion (t=60 min) of TAF1 and TAF2 in human cells, and pol II pausing was disrupted at thousands of genes. Similar results were obtained in TAF1-depleted Drosophila S2 cells. Collectively, these data establish the general transcription factor TFIID as a genome-wide regulator of pol II promoter-proximal pausing.
2020-05-28 | GSE132764 | GEO
Project description:Promoter-proximal RNA polymerase II (Pol II) pausing is implicated in the regulation of gene transcription. However, the mechanisms of pausing including its dynamics during transcriptional responses remain to be fully understood. We performed global analysis of short capped RNAs and Pol II Chromatin Immunoprecipitation sequencing in MCF-7 breast cancer cells to map Pol II pausing across the genome, and used permanganate footprinting to specifically follow pausing during transcriptional activation of several genes involved in the Epithelial to Mesenchymal Transition (EMT). We find that the gene for EMT master regulator Snail (SNAI1), but not Slug (SNAI2), shows evidence of Pol II pausing before activation. Transcriptional activation of the paused SNAI1 gene is accompanied by a further increase in Pol II pausing signal whereas activation of non-paused SNAI2 gene results in the acquisition of a typical pausing signature. The increase in pausing signal reflects increased transcription initiation without changes in Pol II pausing. Activation of the heat shock HSP70 gene involves pausing release that speeds up Pol II turnover, but does not change pausing location. We suggest that Pol II pausing is retained during transcriptional activation and can further undergo regulated release in a signal-specific manner. Untreated MCF-7 cells were analyzed for the distribution of Pol II using ChIP-sequencing with Anti-Pol II N-20 antibody (two independent biological replicates, A, B), and for the distribution of paused RNA polymerase II by sequencing of short capped RNAs (scRNAs) prepared from nuclei (three independent biological replicates, 1-3). All samples were sequenced on a MiSeq instrument in paired-end format
2015-03-27 | E-GEOD-67041 | biostudies-arrayexpress