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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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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.

2019-01-15 | GSE117402 | GEO

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

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2005-10-07 | E-SMDB-2062 | biostudies-arrayexpress

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

2011-07-18 | E-GEOD-30689 | biostudies-arrayexpress

Global timeospatial map of RNA polymerase in Escherichia coli

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

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The Cdk8 kinase module regulates Mediator-RNA polymerase II interaction

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

2011-07-19 | GSE30689 | GEO

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

Genome-wide mapping of RNA Polymerase II binding sites

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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New Chromatin Run-On Reaction Enables Global Mapping of Active RNA Polymerase Locations in an Enrichment-free Manner

Project description:The status of cellular RNA polymerases’ locations mirrors global transcriptional activity. A number of methods have been developed to map the distribution of RNA polymerase II (RNPII) genomewide, most of which took advantages of im-munoprecipitations of RNPII complexes or nucleotide analog-labeled nascent RNAs followed by high-throughput sequenc-ing. Given the tedious procedures involved in enrichment and sequencing library construction experiments, development of a simple method that conquers these issues is highly beneficial to the field. Here we report a mutation-based and enrich-ment-free Global chromatin Run-On sequencing (mGRO-seq) technique to map strand-specific RNPII locations ge-nomewide at near base resolution. An ATP analog, named N6-allyladenosine triphosphate (a6ATP), was designed and incor-porated into nascent RNAs at RNPII-located positions during a chromatin run-on assay. The chromatin RNAs were purified and subjected to a mild iodination reaction, which quantitatively transformed a6A into 1,N6-cyclized adenosine (cyc-A). During reverse transcription of RNA to complementary DNA (cDNA), base misincorporation at opposite site of cyc-A oc-curred and mutation reads were generated in the cDNA high-throughput sequencing. Bioinformatics analysis identified the genomewide RNPII location distributions from the characteristic A-mutated sites. mGRO-seq yields both the profile of RNPII sites and the chromatin RNA abundance from one experiment. To sum up, our work demonstrated a new simple and cost-effective method for mapping RNA polymerase locations genomewide, which holds great promise for single-cell char-acterization of RNPII distributions.

2023-10-25 | GSE160073 | GEO

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