Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Regulation of Pol II pausing is involved in daily transcription in the mouse livers in the mouse liver

ABSTRACT: Purpose: We used ChIP-seq to analyze daily transcription and regulation of Pol II pausing within the mouse liver. Methods: Livers of young mice were processed for Pol II and Nelf-A ChIP-seq at 4-h interval across the day. The binding pattern was analyzed by MACS. Tag pileup within promoter and gene body regions were also obtained to calculate Pol II TR. Results: We obtained > 10 million high quality sequencing reads per time points per sample after quality control and alignments. MACS identified nearly 10,000 Pol II peaks genomewide throughout the day. Nelf-A peaks varied from a few hundreds to 10,000 across the day. A genomewide Nelf-A binding rhythm was evident. We also quantitated bindings within the TSS region and/or gene body and analyzed the quantitation results with ARSER for rhythm detection. We found Pol II binding within the TSS region and gene body show discordant changes. While most genes had peak TSS Pol II binding around dawn, Pol II binding within the gene body showed more scattered distribution, with two peaks around dawn and dusk, respectively. Pol II traveling ratio also showed daily changes, with most genes having a higher TR around dawn. Conclusions: Our study revealed discordant Pol II rhythms in the TSS region and within the gene body, and indicated that Pol II initiation and pause release could have distinct roles in the generation of transcription rhythms within the mouse liver.

ORGANISM(S): Mus musculus

PROVIDER: GSE96773 | GEO | 2018/12/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Regulation of Mammalian Cell Growth and Survival By an RNA Polymerase II-Pausing Factor (ChIP-seq)

Project description:Many mammalian genes are occupied by paused RNA polymerase II (pol II) at promoter-proximal regions on both sides of transcription start sites (TSSs). However, the consequences of pol II pausing on gene expression and cell biology are not fully understood. Here we report that genetic ablation of the b subunit of mouse negative elongation factor (Nelf-b), a key pol II-pausing factor, results in slower progression at multiple cell cycle stages and increased apoptosis. Consistently, a whole-genome analysis indicates that growth and cell death-related genes are highly enriched among the direct target genes of Nelf-b. In particular, Nelf-b deletion increases pol II density in the promoter-distal region of stress response genes and their overall expression levels in the absence of any external stress signals. In addition, our work also reveals a previously unappreciated role of Nelf-b role in curbing TSS-upstream transcription of many mammalian genes. We suggest that Nelf-mediated pol II pausing balances the cellular needs for growth/survival and stress response by preventing excessive basal transcription of stress-induced genes. Examination of Nelf-b bindings sites on chromosomes in mouse embryonic fibroblasts

2011-08-17 | E-GEOD-24113 | biostudies-arrayexpress

NELF regulates a promoter-proximal step distinct from RNA Pol II pause-release

Project description:RNA polymerase II (Pol II) is generally paused at promoter-proximal regions in most metazoans, and based on in vitro studies, this function has been attributed to the negative elongation factor (NELF). Here, we show that upon rapid depletion of NELF, Pol II fails to be released into gene bodies, stopping instead around the +1 nucleosomal dyad-associated region. The transition to the 2nd pause region is independent of positive transcription elongation factor P-TEFb. During the heat shock response, Pol II is rapidly released from pausing at heat shock induced genes, while most genes are paused and transcriptionally downregulated during the heat shock response. We find that both aspects of the heat shock response remain intact upon NELF loss. We find that NELF depletion results in global loss of cap-binding complex from chromatin without global reduction of nascent transcript 5’ cap stability. Thus, our studies implicate NELF functioning in early elongation complexes distinct from Pol II pause-release.

2020-03-09 | GSE144786 | GEO

Regulation of Mammalian Cell Growth and Survival By an RNA Polymerase II-Pausing Factor (Gene expression)

Project description:Many mammalian genes are occupied by paused RNA polymerase II (pol II) at promoter-proximal regions on both sides of transcription start sites (TSSs). However, the consequences of pol II pausing on gene expression and cell biology are not fully understood. Here we report that genetic ablation of the b subunit of mouse negative elongation factor (Nelf-b), a key pol II-pausing factor, results in slower progression at multiple cell cycle stages and increased apoptosis. Consistently, a whole-genome analysis indicates that growth and cell death-related genes are highly enriched among the direct target genes of Nelf-b. In particular, Nelf-b deletion increases pol II density in the promoter-distal region of stress response genes and their overall expression levels in the absence of any external stress signals. In addition, our work also reveals a previously unappreciated role of Nelf-b role in curbing TSS-upstream transcription of many mammalian genes. We suggest that Nelf-mediated pol II pausing balances the cellular needs for growth/survival and stress response by preventing excessive basal transcription of stress-induced genes. Immortalized mouse embryonic fibroblasts derived from a Nelf-b flox/- embryo were infected with control or Cre-epxressing retrovirus. Gene expression profile of control and knockout MEF at 7 days after virus infection were compared by using Illumina's mouse whole-genome gene expression BeadChIPs. There are two replicates for both control and knockout MEF samples.

2011-08-16 | E-GEOD-24114 | biostudies-arrayexpress

BRCA1 Balances the Action of a Transcription Elongation Factor In Mammary Gland Development and Tumorigenesis (sequencing)

Project description:Work from our mouse models showed that COBRA1, the B subunit of NELF, could facilitate R-loop (DNA:RNA hybrid) accumulation in the BRCA1-deficient mouse mammary epithelium. Since NELF could promoter RNA PolII pausing at promoter proximal regions, we asked whether COBRA1-mediated RNA Pol II pausing could contribute to accumulated R-loops. To answer this question, we performed chromatin immunoprecipitation-sequencing (ChIP-seq) for RNA Pol II, as well as two NELF subunits, NELF-A and NELF-B (COBRA1) in mouse primary mammary epithelium cells. To locate R-loops in the same cell population, we performed DNA:RNA immunoprecipitation-sequencing (DRIP-seq) with or without treatment of RNase H, a nuclease that specifically degrades RNA in the R-loop structure. Our sequencing results showed that RNA Pol II, NELF and R-loops are all enriched at transcription start sites (TSSs). Notably, genes with TSS R-loop accumulation are significantly enriched for COBRA1 binding. Taken together, the genomic data lent additional support to the notion that COBRA1-mediated RNAPII pausing contributes to R-loop dynamics in mammary epithelium.

2021-03-30 | GSE67702 | GEO

Regulation of Mammalian Cell Growth and Survival By an RNA Polymerase II-Pausing Factor (Gene expression)

2011-08-17 | GSE24114 | GEO

Regulation of Mammalian Cell Growth and Survival By an RNA Polymerase II-Pausing Factor (ChIP-seq)

2011-08-17 | GSE24113 | GEO

Paf1C regulates RNA polymerase II progression by modulating elongation rate

Project description:Elongation factor Paf1C regulates several stages of the RNA polymerase II (Pol II) transcription cycle, although it is unclear how it modulates Pol II distribution and progression in mammalian cells. We found that conditional ablation of Paf1 resulted in the accumulation of unphosphorylated and Ser5 phosphorylated Pol II around promoter proximal regions and within the first 20-30 kb of gene bodies, respectively. Paf1 ablation did not impact the recruitment of other key elongation factors, namely, Spt5, Spt6, and the FACT complex, suggesting that Paf1 function may be mechanistically distinguishable from each of these factors. Moreover, loss of Paf1 triggered an increase in TSS-proximal nucleosome occupancy, which could impose a considerable barrier to Pol II elongation past TSS-proximal regions. Remarkably, accumulation of Ser5P in the first 20-30 kb coincided with reductions in histone H2B ubiquitylation within this region. Furthermore, we show that nascent RNA species accumulate within this window, suggesting a mechanism whereby Paf1 loss leads to aberrant, prematurely terminated transcripts and diminution of full-length transcripts. Importantly, we found that loss of Paf1 results in Pol II elongation rate defects with significant rate compression. Our findings suggest that Paf1C is critical for modulating Pol II elongation rates by functioning beyond the pause-release step as an "accelerator" over specific early gene body regions.

2019-06-28 | GSE116169 | GEO

Genome-wide map of RNA polymerase II, NELF, and DSIF in HeLa cells

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

The NELF pausing checkpoint mediates the functional divergence of Cdk9

Project description:Cdk9 is an essential transcriptional kinase that is conserved across distant eukaryotes, but we previously found that acute inhibition of Cdk9 causes different transcriptional phenotypes in NELF-containing higher eukaryotes (like mammals and Drosophila) vs. the NELF-lacking fission yeast S. pombe. NELF is known to participate in promoter-proximal pausing of RNA Polymerase II, and using NELF-depleted Drosophila cells, we find that this NELF-mediated pause is necessary to prevent gene body entry by Pol II in the absence of Cdk9. Without NELF, the abnormal gene body entry that occurs following Cdk9 inhibition is strikingly similar to that seen in S. pombe, and in either case, these Pol II complexes have elongation defects and are unable to complete gene transcription. These results show that NELF enforces an early checkpoint for Cdk9 and efficiently shuts down gene transcription in its absence. We propose this would have been critical for the emergence of gene regulatory strategies acting via Cdk9 to modulate transcription of specific genes.

2023-03-22 | GSE211397 | GEO

Postrecruitment Regulation of RNA Pol II Directs Rapid Signaling Responses at the Promoters of Estrogen Target Genes

Project description:Under current models for signal-dependent transcription in eukaryotes, DNA-binding activator proteins regulate the recruitment of RNA polymerase II (Pol II) to a set of target promoters. Yet, recent studies, as well as our results herein, show that Pol II is widely distributed (i.e., "preloaded") at the promoters of many genes prior to specific signaling events. How Pol II recruitment and Pol II preloading fit within a unified model of gene regulation is unclear. In addition, the mechanisms through which cellular signals activate preloaded Pol II across mammalian genomes remain largely unknown. Here we show that the predominant genomic outcome of estrogen signaling is the post-recruitment regulation of Pol II activity through phosphorylation, rather than recruitment of Pol II. Furthermore, we show that negative elongation factor (NELF) binds to estrogen target promoters in conjunction with preloaded Pol II and represses gene expression until the appropriate signal is received. Finally, our studies reveal that the estrogen-dependent activation of preloaded Pol II facilitates rapid transcriptional and post-transcriptional responses which play important physiological roles in regulating estrogen signaling itself. Our results reveal a broad use of post-recruitment Pol II regulation by the estrogen signaling pathway, a mode of regulation that is likely to apply to a wide variety of signal-regulated pathways. ChIP-chip analysis for RNA Pol II, Ser5 phosphorylated RNA Pol II and NELF-A in MCF7 breast cancer cells.

2010-05-14 | E-GEOD-13051 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data