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Homo sapiens

ABSTRACT: Genome-wide map of Pol II and Flag-LARP7 in human HeLa cells

PROVIDER: PRJNA344878 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4304562_1.fastq.gz	Fastqsanger.gz
	SRR4304562_2.fastq.gz	Fastqsanger.gz
	SRR4304563_1.fastq.gz	Fastqsanger.gz
	SRR4304563_2.fastq.gz	Fastqsanger.gz
	SRR4304564_1.fastq.gz	Fastqsanger.gz

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Genome-wide map of Pol II and Flag-LARP7 in human HeLa cells

Project description:We generated genome-wide maps of Pol II and Flag-LARP7 in human HeLa cells. We find that Flag-LARP7 and Pol II co-locolize on Pol II-specific sn/snoRNA genes.

2017-02-02 | GSE87470 | GEO

Homo sapiens

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

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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

Effect of splicing on histone H3 K36 methylation

Project description:Histone H3 K36me3 and RNA pol II were localized by ChIP before and after inhibition of splicing by spliceostatin for 12 hr. Total matched reads for the control and SSA treated Hela samples were 11.6 and 8.2 million for anti-H3K36me3 and 6.6 and 5.0 million for anti-pol II. ChIP-seq of histone H3 K36me3 and RNA pol II in Hela cells before and after spliceosotatin treatment

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Pol II and its associated epigenetic marks are present at pol III-transcribed non-coding RNA genes (I)

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. Chip-Seq experiments for six samples: Pol III, TFIIIB, TFIIIC, H3K4me3 in HeLa cells and Pol III, S2 phos Pol II in CD4+ cells.

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Mitotic Transcriptional Clearance of Actively Engaged Pol II Through Transcriptional Elongation Control

Project description:Chromatin is highly condensed and transcriptionally repressed during mitosis. Although it is established that some general transcription factors are inactivated by phosphorylation at mitosis, many details of mitotic transcriptional repression and its underlying mechanisms are largely unknown. Here, we provide evidence that as cells enter mitosis, genes with transcriptionally engaged RNA Polymerase II (Pol II) can continue transcription until the end of the gene to clear Pol II from mitotic chromatin. Using ChIP-Seq, we find that the transcriptional reinitiation process is globally impaired in early mitosis (prophase/prometaphase), with loss of TFIIB occupancy and nucleosome-free regions at promoters. Pretreatment of nocodazole-arrested mitotic cells with the P-TEFb inhibitor flavopiridol prevents the release of promoter-proximal engaged Pol II. Global nascent RNA sequencing and RNA fluorescence in situ hybridization (FISH) of individual genes demonstrate the existence of transcriptionally engaged Pol II in early mitosis. Chemical and mutational inhibition of P-TEFb in mitosis leads to delays in the progression of cell division. Together, our study reveals a novel mechanism for mitotic transcriptional repression whereby transcriptionally engaged Pol II can progress into productive elongation and finish transcription to allow proper cellular division. ChIP-Seq of Pol II of different forms, TFIIB, H3K4me3 in human HeLa cells at different cell cycle stages. ChIP-Seq of Pol II in HeLa mitotic cells with or without CDK9 inhibitor flavopiridol pretreatment. Nascent RNA-seq in asynchronous and arrested mitotic cells.

2015-10-30 | E-GEOD-71848 | biostudies-arrayexpress

ChIP-seq analysis of HeLa cancer stem cells and non-cancer stem cells using Pol II, H3K4me3 and H3K27Ac.

Project description:ChIP-seq analysis of HeLa cancer stem cells and non-cancer stem cells regarding Pol II, H3K4me3 and H3K27Ac.

2018-11-29 | GSE103187 | GEO

Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors.

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

Homo sapiens

Project description:Genome-wide chromatin binding of MYC, Omomyc, RNA polymerase II (Pol II), and Pol II Ser-2p in human glioblastoma cells and glioblastoma stem cells expressing or not Omomyc

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Multiorgan PIXUL-ChIP-seq analysis of genome-wide RNA polymerase II (Pol II) binding in mouse heart, kidney, liver and lung

Project description:High throughput PIXUL-ChIP-seq genome-wide study allows to map simultaneously Pol II peaks in multiple organs harvested from the same mouse.

2018-06-19 | GSE100348 | GEO

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