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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

SUBMITTER: Iouri Chepelev

PROVIDER: E-GEOD-20071 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Pol II and its associated epigenetic marks are present at Pol III-transcribed noncoding RNA genes.

Barski Artem A Chepelev Iouri I Liko Dritan D Cuddapah Suresh S Fleming Alastair B AB Birch Joanna J Cui Kairong K White Robert J RJ Zhao Keji K

Nature structural & molecular biology 20100425 5

Epigenetic control is an important aspect of gene regulation. Despite detailed understanding of protein-coding gene expression, the transcription of noncoding RNA genes by RNA polymerase III (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 al ...[more]

PMID: 20418881

Similar Datasets

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.

2010-04-25 | E-GEOD-20040 | biostudies-arrayexpress

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

2010-04-25 | GSE20071 | GEO

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

2010-04-25 | GSE20040 | GEO

Chromatin remodeling by antisense Pol II primes efficient Pol III transcription

Project description:The packaging of the genetic material into chromatin imposes the remodeling of this barrier to allow efficient transcription. RNA polymerase II activity is associated with several histone modification complexes that enforce remodeling. How RNA polymerase III (Pol III) counteracts the inhibitory effect of chromatin is unknown. We report here that antisense RNA Polymerase II (Pol II) transcription is critical to prime and maintain nucleosome depletion at Pol III loci and allow efficient Pol III recruitment upon re-initiation of growth from stationary phase. Antisense Pol II is recruited by the Pcr1 transcription factor, which affects local histone occupancy through the associated SAGA complex and a Pol II phospho-S2 CTD / Mst2 pathway. These data expand the central role of Pol II in gene expression beyond mRNA synthesis.

2022-12-24 | GSE193552 | GEO

RNA Pol III transcriptomes and relationships to Pol II promoters, enhancer-binding factors and chromatin domains

Project description:RNA polymerase III transcribes many noncoding RNAs (e.g. tRNAs) important for translational capacity and other functions. Here, we localized RNA polymerase III, alternative TFIIIB complexes (BRF1/2) and TFIIIC in HeLa cells, determining the Pol III transcriptome, defining gene classes, and revealing ‘TFIIIC-only’ sites. Pol III localization in other transformed and primary cell lines revealed both novel and cell-type specific Pol III loci, and one occupied miRNA. Surprisingly, only a fraction of the in silico-predicted Pol III loci are occupied. Interestingly, 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. Remarkably, Pol III occupancy scales with the levels of nearby Pol II, active chromatin and CpG content. Taken together, active promoter and enhancer-like chromatin appears to gate Pol III accessibility to the genome.

2010-04-14 | GSE20609 | GEO

RNA Pol III transcriptomes and relationships to Pol II promoters, enhancer-binding factors and chromatin domains

2010-04-14 | E-GEOD-20609 | biostudies-arrayexpress

Pol III transcribed genes, RNA-Seq, C.elegans

Project description:RNA-Seq of small (Pol III-transcribed) RNAs in worms, Pol III RNAi versus control

2024-08-26 | GSE232720 | GEO

Chromatin remodeling by antisense Pol II primes efficient Pol III transcription

Project description:Chromatin remodeling by antisense Pol II primes efficient Pol III transcription

| PRJNA796588 | ENA

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.

2010-04-14 | GSE20309 | GEO

RSC Regulates Nucleosome Positioning at Pol II Genes and Density at Pol III Genes

Project description:Nucleosomes restrict the access of transcription factors to chromatin. RSC is a SWI/SNF-family chromatin-remodeling complex from yeast that repositions and ejects nucleosomes in vitro. Here, we examined these activities and their importance in vivo. We utilized array-based methods to examine nucleosome occupancy and positioning at more than 200 locations in the genome following the controlled destruction of the catalytic subunit of RSC, Sth1. Loss of RSC function caused pronounced and general reductions in transcription from Pol I, II, and III genes. At Pol III genes, Sth1 loss conferred a general gain in nucleosome density and an accompanying reduction in RNA Pol III occupancy. In contrast, we observed primarily single nucleosome changes, including movement, at Pol II promoters. Importantly, a greater number of changes were observed near the transcription start sites of RSC-occupied promoters than non-occupied promoters. These changes are distinct from those due to general loss of transcription. Thus, RSC action affects both nucleosome density and positioning in vivo, but applies these remodeling modes differently at Pol II and Pol III genes. Keywords: ChIP-chip, nucleosome, mononucleosome, RSC, transcription

2007-12-01 | GSE8862 | GEO

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