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Genome-wide map of RNA polymerase II enrichment in Wild-Type and Ipa1-1 mutant samples

ABSTRACT: Genome-wide map of RNA polymerase II enrichment in Wild-Type and Ipa1-1 mutant samples

PROVIDER: PRJNA481992 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7543010.fastq.gz	Fastqsanger.gz
	SRR7543011.fastq.gz	Fastqsanger.gz
	SRR7543012.fastq.gz	Fastqsanger.gz
	SRR7543013.fastq.gz	Fastqsanger.gz
	SRR7543006.fastq.gz	Fastqsanger.gz

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Genome-wide map of RNA polymerase II enrichment in Wild-Type and Ipa1-1 mutant samples

Project description:We report on a comparison of ChIP-seq comparison of wild-type (BY4741) and Ipa1-1 mutant yeast, using duplicate samples of each genotype. Our analysis shows that loss of Ipa1 function leads to loss of 3'-end formation, and specifically shows a distinct gain of occupancy immediately downstream of polyA sites, suggesting that inefficient cleavage is causing PolII to remain attached ot the genomic DNA for relatively longer periods of time.

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Genome wide demarcation of RNA Polymerase II transcription Uuits Rrevealed by physical fractionation of chromatin- neutral enrichment

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Enrichment profiles of Ser-5 phosphorylated RNA polymerase II (PolII S5p) in mouse female ES cells

Project description:Many animal species employ a chromosome-based mechanism of sex determination, which has led to coordinate evolution of dosage compensation systems. Dosage compensation not only corrects the imbalance in the number of X-chromosomes between the sexes, but is also hypothesized to correct dosage imbalance within cells due to mono-allelic X expression and bi-allelic autosomal expression, by upregulating X-linked genes (termed ‘Ohno’s hypothesis’). It is unknown whether any epigenetic mark or protein is involved in X upregulation in mammals. Ser-5 phosphorylated RNA polymerase II (PolII S5p) is required for transcription initiation. Chromatin immunoprecipitation combined with DNA tiling array analysis (ChIP-chip) of PolII S5p in mouse female ES cells with two active X chromosomes demonstrated a greater enrichment of RNA polymerase II on X-linked genes relative to autosomal genes, suggesting that enhanced transcription initiation may play a role in X upregulation. Comparison of RNA PolII S5p enrichment on the X versus autosomes in mouse

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Project description:Global timeospatial map of RNA polymerase in Escherichia coli

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Project description:We use biochemically reconstituted transcription initiation components including the Mediator core and Cdk8 kinase modules (CKM) to investigate the function of the CKM in regulating the Mediator-RNA polymerase II interaction in a highly purified system. We use cross-linking coupled to mass spectrometry to map the interaction of the CKM and core Mediator, and in vitro phosphorylation assays followed by phosphopeptide enrichment coupled to mass spectrometry to identify Cdk8 phosphorylation targets in this context and biochemically dissect their functions. Finally, we investigate the function of phosphorylation by Cdk8 on transcription in vivo. Based on that, we propose a model to integrate the phosphorylation-dependent and -independent functions of the CKM in transcription initiation.

2021-04-28 | PXD023361 | Pride

Enrichment profiles of Ser-5 phosphorylated RNA polymerase II (PolII S5p) in mouse female ES cells

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Genome-wide profiling (ChIP-seq) of RNA polymerase II in wild-type, fpa mutant and bdrs triple mutant

Project description:We used 3 different antibodies targeting the YSPTSPS repeats of the C-terminal domain (CTD) of the Rpb1 subunit of RNA polymerase II (ab817: non phosphorylated repeats, ab5095: phospho Ser2 repeats and ab5131: phospho Ser5 repeats) to obtain genome-wide profiles by ChIP-seq of the localization of RNA polymerase II in wild-type (Col-0), fpa mutant (fpa/AT2G43410, line fpa-7) and a triple mutant of all three BDR proteins (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). We found that BDR proteins are involved in RNA polymerase II 3' pausing and that their deletion generates transcriptional interferences in closely spaced, tandemly organized, gene pairs.

2019-08-08 | GSE113078 | GEO

Genome wide demarcation of RNA Polymerase II transcription units revealed by physical fractionation of chromatin- neutral enrichment (ORF+intergenic enrichment

Project description:Genome-wide Demarcation of RNA Polymerase II Transcription Units Revealed by Physical Fractionation of Chromatin - ORF + Intergenic_enrichment

2005-10-07 | E-SMDB-2065 | biostudies-arrayexpress

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Project description:Protein coding genes and some of the non-coding RNA genes in eucaryotes are transcribed by RNA Polymerase II. A transcription machinery complex consists of RNA Pol II and many other proteins including transcription factors, activators and repressors of transcription. Pol II binding sites are found in actively transcribing genes and many which are not actively transcribing. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Map binding sites of RNA Polymerase II in the genome of K562 & NB4 cells

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Genome-wide association of mediator and RNA polymerase II in wild-type and mediator mutant yeast.

Project description:Mediator is a large, multisubunit complex that is required for essentially all mRNA transcription in eukaryotes. In spite of the importance of Mediator, the range of its targets and how it is recruited to these is not well understood. Previous work showed that in Saccharomyces cerevisiae, Mediator contributes to transcriptional activation by two distinct mechanisms, one depending on the tail module triad and favoring SAGA-regulated genes, and the second occurring independently of the tail module and favoring TFIID-regulated genes. Here, we use chromatin immunoprecipitation sequencing (ChIP-seq) to show that dependence on tail module subunits for Mediator recruitment and polymerase II (Pol II) association occurs preferentially at SAGA-regulated over TFIID-regulated genes on a genome-wide scale. We also show that recruitment of tail module subunits to active gene promoters continues genome-wide when Mediator integrity is compromised in med17 temperature-sensitive (ts) yeast, demonstrating the modular nature of the Mediator complex in vivo. In addition, our data indicate that promoters exhibiting strong and stable occupancy by Mediator have a wide range of activity and are enriched for targets of the Tup1-Cyc8 repressor complex. We also identify a number of strong Mediator occupancy peaks that overlap dubious open reading frames (ORFs) and are likely to include previously unrecognized upstream activator sequences.

| S-EPMC4295389 | biostudies-literature

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