Multiorgan PIXUL-ChIP-seq analysis of genome-wide RNA polymerase II (Pol II) binding in mouse heart, kidney, liver and lung
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE100348 | GEO | 2018/06/19
REPOSITORIES: GEO
Similar Datasets
Project description:When challenged with osmotic shock, S. cerevisiae induces hundreds of genes, despite a global reduction in transcriptional capacity. The mechanisms that regulate this rapid reallocation of transcriptional resources are not known. Here we show that redistribution of RNA Pol II upon stress requires the stress-responsive MAP kinase Hog1. We find that Hog1 and RNA Pol II co-localize to open reading frames that bypass global transcriptional repression, and that these targets are specified by two osmotic stress-responsive transcription factors. The combination of reduced global transcription with a gene-specific override mechanism allows cells to rapidly switch their transcriptional program in response to stress. ChIP-sequencing of S. cervisiae RNA Pol II, Hog1, Sko1 and Hot1 Processed data file descriptions: ORFcounts.txt: table of summed ChIP-seq reads that align to each ORF (normalized by reads per kilobase per million) promoter_counts.txt: table of summed ChIP-seq reads that align to each promoter (1kb upstream, normalized by reads per kilobase per million) downstream_counts.txt: table of summed ChIP-seq reads that align 3' regions (50-500 bp downstream, normalized by reads per kilobase per million) Sko1_peak_list.txt: table of peaks found by PeakSeq Hot1_peak_list.txt: table of peaks found by PeakSeq
2012-07-15 | E-GEOD-38208 | biostudies-arrayexpress
Project description:RNA polymerase II (Pol II) subunits are thought to be involved in various transcription-associated processes, but it is unclear whether they play different regulatory roles in modulating gene expression. Here, we performed nascent and mature transcript sequencing after the acute degradation of 12 mammalian Pol II subunits and profiled their genomic binding sites and protein interactomes to dissect their molecular functions. We found that Pol II subunits contribute differently to Pol II cellular localization and transcription process and preferentially regulate RNA processing (such as RNA splicing and 3’ end maturation). Genes sensitive to the depletion of different Pol II subunits tend to be involved in diverse biological functions and show different RNA half-lives. Sequences, associated protein factors, and RNA structures are correlated with Pol II subunit-mediated differential gene expression. These findings collectively suggest that the heterogeneity of Pol II and different genes appear to depend on some of the subunits.
2022-08-09 | PXD035866 |
Project description:RNA polymerase (Pol) III transcribes many noncoding RNAs (for example, transfer RNAs) important for translational capacity and other functions. We localized Pol III, alternative TFIIIB complexes (BRF1 or BRF2) and TFIIIC in HeLa cells to determine the Pol III transcriptome, define gene classes and reveal 'TFIIIC-only' sites. Pol III localization in other transformed and primary cell lines reveals previously uncharacterized and cell type–specific Pol III loci as well as one microRNA. Notably, only a fraction of the in silico–predicted Pol III loci are occupied. Many occupied Pol III genes reside within an annotated Pol II promoter. Outside of Pol II promoters, occupied Pol III genes overlap with enhancer-like chromatin and enhancer-binding proteins such as ETS1 and STAT1. Moreover, Pol III occupancy scales with the levels of nearby Pol II, active chromatin and CpG content. These results suggest that active chromatin gates Pol III accessibility to the genome. Use of ChIP-seq to identify genomic regions bound by RNA Polymerase III machinery in multiple cell types as well as RNA-seq in HeLa for gene expression analysis. See GSE20609 for whole human genome raw Pol III ChIP-array data. See link below for supplementary methods and analysis.
2010-04-14 | E-GEOD-20309 | biostudies-arrayexpress
Project description: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.
2018-12-20 | GSE96773 | GEO
Project description:RNA polymerase (Pol) III transcribes many noncoding RNAs (for example, transfer RNAs) important for translational capacity and other functions. We localized Pol III, alternative TFIIIB complexes (BRF1 or BRF2) and TFIIIC in HeLa cells to determine the Pol III transcriptome, define gene classes and reveal 'TFIIIC-only' sites. Pol III localization in other transformed and primary cell lines reveals previously uncharacterized and cell type–specific Pol III loci as well as one microRNA. Notably, only a fraction of the in silico–predicted Pol III loci are occupied. Many occupied Pol III genes reside within an annotated Pol II promoter. Outside of Pol II promoters, occupied Pol III genes overlap with enhancer-like chromatin and enhancer-binding proteins such as ETS1 and STAT1. Moreover, Pol III occupancy scales with the levels of nearby Pol II, active chromatin and CpG content. These results suggest that active chromatin gates Pol III accessibility to the genome.
2010-04-14 | GSE20309 | GEO
Project description:Transcription of the eukaryotic genomes is carried out by three distinct RNA polymerases I, II and III whereby each polymerase is thought to independently transcribe a distinct set of genes. To investigate a possible relationship of RNA polymerases II and III we mapped their in vivo binding sites throughout the human genome using ChIP Seq in two different cell lines, GM12878 and K562 cells. Pol III was found to bind near many known genes as well as several novel genes. RNA-Seq studies indicate that majority of the genes are expressed although a subset are not suggestive of stalling by RNA polymerase III. Pol II was found to bind near many known Pol III genes, including tRNA, U6, HVG, hY and 7SK and novel Pol III genes. Similarly, in vivo binding studies also reveal that a number of transcription factors normally associated with Pol II transcription, including c-Fos, c-Jun and c-Myc, also tightly associate with most Pol III transcribed genes. Inhibition of Pol II activity using ?-amanitin reduced expression of a number of Pol III genes (e.g. U6, hY, HVG), suggesting that Pol II plays an important role in regulating their transcription. These results indicate that, contrary to previous expectations, polymerases can often work with one another to globally coordinate gene expression. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf This SuperSeries is composed of the SubSeries listed below.
2009-12-31 | GSE19551 | GEO
Project description:Aim: To determine RNA Pol II binding sites in mouse heart and liver, 4 hours post MycER activation. Pol II ChIP sequencing performed on chromatin isolated from hearts and livers harvested from wild-type (R26+/+) and R26CAG-c-MycERT2/+ mice 4 hours post administration of (Z)-4-hydroxytamoxifen.
2020-03-06 | E-MTAB-7593 | biostudies-arrayexpress
Project description:The protein Vezf1 plays multiple roles important for embryonic development. In Vezf1-/- mouse embryonic stem (MES) cells our earlier data showed widespread changes in gene expression profiles, including decreased expression of the full length active isoform of Dnmt3b methyltransferase and concomitant genome wide reduction in DNA methylation. Here we show that, in HeLaS3 cells, there is a strong genome-wide correlation between Vezf1 binding and peaks of elongating Ser2-P Pol ll, reflecting Vezf1 dependent slowing of elongation. In Wt MES cells the elongating form of RNA polymerase II accumulates near Vezf1 binding sites within the dnmt3b gene and at several other Vezf1 sites, and this accumulation is significantly reduced at these sites in Vezf1-/- MES cells. Depending upon genomic location, Vezf1 mediated Pol II pausing can have different regulatory roles in transcription and splicing. We find examples of genes in which Vezf1 binding sites are located near cassette exons, and in which loss of Vezf1 leads to a change in the relative abundance of alternatively spliced messages. We further show that Vezf1 interacts with Mrg15/Mrgbp, a protein that recognizes H3K36 tri-methylation, consistent with the role of histone modifications at alternatively spliced sites. Comparison of Vezf1 and RNA Pol II binding in mouse and human cells.
2012-03-09 | E-GEOD-34785 | biostudies-arrayexpress
Project description:Epigenetic control is an important aspect of gene regulation. Despite detailed understanding of many examples, the transcription of non-coding RNA genes by RNA polymerase (pol) III is less well characterized. Here we profile the epigenetic features of pol III target genes throughout the human genome. This reveals that the chromatin landscape of pol III-transcribed genes resembles that of pol II templates in many ways, although there are also clear differences. Our analysis also discovered an entirely unexpected phenomenon, namely that pol II co-localizes with the majority of genomic loci that are bound by pol III. RNA-seq experiment for total RNA in CD4+ cells.
2010-04-25 | E-GEOD-20071 | biostudies-arrayexpress