PRO-seq for Pol II occupancy project
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ABSTRACT:
PROVIDER: PRJEB80139 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Amplicon SMF for Pol II occupancy project
| PRJEB80138 | ENA
Project description:Protein phosphatase 1 complex (PP1C), consisting of one of the phosphatases, PP1α, β and γ, and three regulatory subunits PNUTS, TOX4 and WDR82, plays critical roles in gene regulation and is mutated in over 20% uterine corpus endometrial carcinoma cases. Here we show that knockdown of PP1γ reduced chromatin occupancy of RNA polymerase II (Pol II), but increased the cellular level and chromatin occupancy of Ser-2 phosphorylated Pol II and Ser-5 phosphorylated Pol II. 4sUDRB-seq data showed that the Pol II elongation rate decreased upon PP1γ loss. These results advanced our understanding of the roles of PP1γ in transcriptional regulation.
2025-03-09 | GSE198200 | GEO
Project description:Amplicon Single Molecule Footprinting (SMF) data. SMF data is obtained by treating extracted nuclei with a GpC and a CpG methyltransferases, where binding of proteins on DNA, e.g. nucleosomes and RNA Polymerase II (Pol II), leave behind unmethylated cytosines as footprints. Data in this experiment comprises SMF data obtained from DNA methyltransferase triple knockout mouse embryonic stem cells (DNMT TKO mESCs) treated with either 500 nM triptolide for 30 minutes or DMSO as a control.
2025-01-18 | E-MTAB-14461 | biostudies-arrayexpress
Project description:In mammalian cells, widespread acceleration of cytoplasmic mRNA degradation is linked to impaired RNA polymerase II (Pol II) transcription. This mRNA decay-induced transcriptional repression occurs during infection with gammaherpesviruses including Kaposi’s sarcoma associated herpesvirus (KSHV) and murine gammaherpesvirus 68 (MHV68), which encode an mRNA endonuclease that initiates widespread RNA decay. Here, we show that MHV68-induced mRNA decay leads to a genome-wide reduction of Pol II occupancy at mammalian promoters. Viral genes, despite the fact that they require Pol II for transcription, escape this transcriptional repression. Protection is not governed by viral promoter sequences; instead, location on the viral genome is both necessary and sufficient to escape the transcriptional repression effects of mRNA decay. We hypothesize that the ability to escape from transcriptional repression is linked to the localization of viral DNA in replication compartments, providing a means for these viruses to counteract decay-induced viral transcript loss.
2019-12-10 | PXD015786 | Pride
Project description:PP1γ regulates Pol II occupancy and elongation rate
| PRJNA814205 | ENA
Project description:We used RNA Pol II-CTD occupancy assay to identify mRNA isoform switch in mutant animals compared to wild type animals. Examination of RNA Pol II-CTD Ser5P recognized by 4H8 in wild type, sydn-1(0), ssup-72(0) and ssup-72(0);sydn-1(0)
2015-11-01 | E-GEOD-68203 | biostudies-arrayexpress
Project description:ATP-dependent chromatin remodelers regulate chromatin structure during multiple stages of transcription. We report that RSC, an essential chromatin remodeler, is recruited to the open reading frames (ORFs) of actively transcribed genes genome-wide, suggesting a role for RSC in regulating transcription elongation. Consistent with such a role, Pol II occupancy in the ORFs of weakly transcribed genes is drastically reduced upon depletion of the RSC catalytic subunit Sth1. RSC inactivation also reduced histone H3 occupancy across transcribed regions. Remarkably, the strongest effects on Pol II and H3 occupancy were confined to the genes displaying the greatest RSC ORF enrichment. Additionally, RSC recruitment to the ORF requires the activities of the SAGA and NuA4 HAT complexes and is aided by the activities of the Pol II CTD Ser2 kinases Bur1 and Ctk1. Overall, our findings strongly implicate ORF-associated RSC in governing Pol II function and in maintaining chromatin structure over transcribed regions. ChIP-chip experiments to measure Sth1, Rpb3 and H3 occupancy in WT and various mutants (histone acetyltransferase and Pol II CTD kinase mutants). The histone H3 and Rpb3 occupancy were also measured in cells upon Sth1 depletion.
2014-11-24 | GSE62519 | GEO
Project description:Precision Run-On Sequencing (PROseq) performed as previously described (Kwak et al., 2013; Judd et al., 2020) with slight modifications. Data is obtained from 1) DNA methyltransferase triple knockout mouse embryonic stem cells (DNMT TKO mESCs) and 2) Drosophila Schneider's S2 cell line. For the Drosophila S2 cell samples, 10 million Drosophila S2 cells were used per sample with a spike-in of 0.1 million (1%) TKO mESCs. For the TKO mESC samples, 5 million TKO mESCs were used per sample with a spike-in of 0.05 million (1%) Drosophila S2 cells. Treatment samples were treated with 10 microM triptolide for various time points (2.5, 5, 10, or 20 minutes). Control samples were treated with DMSO for 20 minutes. PROseq data was obtained by permeabilising the cells, performing a 2 biotin run-on reaction using biotin-11-UTP and biotin-11-CTP and subsequent enrichments steps for biotinylated RNA during the library preparation
2025-01-18 | E-MTAB-14462 | biostudies-arrayexpress
Project description:ATP-dependent chromatin remodelers regulate chromatin structure during multiple stages of transcription. We report that RSC, an essential chromatin remodeler, is recruited to the open reading frames (ORFs) of actively transcribed genes genome-wide, suggesting a role for RSC in regulating transcription elongation. Consistent with such a role, Pol II occupancy in the ORFs of weakly transcribed genes is drastically reduced upon depletion of the RSC catalytic subunit Sth1. RSC inactivation also reduced histone H3 occupancy across transcribed regions. Remarkably, the strongest effects on Pol II and H3 occupancy were confined to the genes displaying the greatest RSC ORF enrichment. Additionally, RSC recruitment to the ORF requires the activities of the SAGA and NuA4 HAT complexes and is aided by the activities of the Pol II CTD Ser2 kinases Bur1 and Ctk1. Overall, our findings strongly implicate ORF-associated RSC in governing Pol II function and in maintaining chromatin structure over transcribed regions. ChIP-chip experiments to measure Sth1, Rpb3 and H3 occupancy in WT and various mutants (histone acetyltransferase and Pol II CTD kinase mutants). The histone H3 and Rpb3 occupancy were also measured in cells upon Sth1 depletion. The WT and mutant strains were grown in Synthetic complete or YPD media to an O.D. 600 of 0.6-0.8. For inducing Gcn4, the cells grown in SC were treated with Sulfometuron methyl for 20-25 minutes and process for chromatin immunoprecipitation using antibodies again Myc, Rpb3 or histone H3.
2014-11-24 | E-GEOD-62519 | biostudies-arrayexpress
Project description:We used RNA Pol II-CTD occupancy assay to identify mRNA isoform switch in mutant animals compared to wild type animals.
2015-11-01 | GSE68203 | GEO