Transcriptional regulation of tDNA in H9 ESCs
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus Homo sapiens
PROVIDER: GSE94418 | GEO | 2020/02/02
REPOSITORIES: GEO
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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. Use of ChIP-array to identify genomic regions bound by RNA Polymerase III machinery
2010-04-14 | E-GEOD-20609 | biostudies-arrayexpress
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
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
Project description:Many regulatory proteins and complexes have been identified which influence transcription by RNA polymerase (pol) II with a fine precision. In comparison, only a few regulatory proteins are known for pol III, which transcribes mostly house-keeping and non-coding RNAs. Yet, pol III transcription is precisely regulated under various stress conditions like starvation. We used proteomic approaches and pol III transcription complex components TFIIIC (Tfc6), pol III (Rpc128) and TFIIIB (Brf1) as baits to find identify the potential interactors through mass spectrometry-based proteomics. A large number of proteins were found in the interactome, which includes known chromatin modifiers, factors and regulators of transcription by pol I and pol II.
2019-01-02 | PXD003748 | Pride
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
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
Project description:RNA polymerase (RNA Pol) III synthesizes the tRNAs, the 5S ribosomal RNA and a small number of untranslated RNAs. In vitro, it also transcribes short interspersed nuclear elements (SINEs). We investigated the distribution of RNA Pol III and its associated transcription factors on the genome of mouse embryonic stem (ES) cell using a highly specific tandem ChIP-Seq method. Only a subset of the annotated class-III genes was bound and thus transcribed. A few hundred SINEs were associated with the RNA Pol III transcription machinery. We observed that RNA Pol III and its transcription factors were present at thirty unannotated sites on the mouse genome, only one of which was conserved in human. An RNA was associated with more than 80% of these regions. More than 2200 regions bound by TFIIIC transcription factor were devoid of RNA Pol III. These sites are correlated with association of CTCF and the cohesin. Cohesin has been shown to occupy sites bound by CTCF and to contribute to DNA loop formation associated with gene repression or activation. This observation suggests that TFIIIC may play a role in chromosome organization in mouse. We also investigated the genome-wide distribution of the ubiquitous TFIIS variant, TCEA1. We found that, as in Saccharomyces cerevisiae, TFIIS is associated with class III genes and also with SINEs suggesting that TFIIS is a RNA Pol III transcription factor in mammals. We performed ChIP-seq experiment on mouse ES cells, in order to analyse the distribution of the RNA Pol III, with two of its subunits, RPC1 and RPC4, of the two distinct forms of the transcription factor TFIIIB, with BRF1 and BRF2, respectively subunit of TFIIIB-beta, and TFIIIB-alpha form, and three subunits of the transcription factor TFIIIC, TFIIIC90, TFIIIC110, TFIIIC220. We also analysed the distribution of the RNA Pol II elongation factor TCEA1. We used tagged proteins, in order to develop a highly specific and generic ChIP-seq protocol. A sequence encoding a 6 histidine-Flag-HA tag was inserted just after the last codon of the gene encoding proteins of the RNA Pol III machinery subunits, or just after the start codon for TCEA1, using the recombineering technology. Untagged ES cell line was used as negative control for data processing. Our dataset comprises of ten ChIP-seq samples, eight from tagged proteins, two from untagged cell line.
2011-09-16 | E-MTAB-767 | biostudies-arrayexpress
Project description:Transcriptional regulation of tDNA in H9 ESCs
| PRJNA369653 | ENA
Project description:Here we report the derivation of human haploid ESCs from parthenogenetic haploid embryos. We used RNA-seq to compare the gene expression levels among human parthenogenetic haploid ESCs (hPGES), normal human ESCs (H9) and human forskin fibroblasts and identified that these cells express conventional ESCs pluripotent markers and most maternally imprinted genes were down-regulated.
2016-07-13 | GSE80988 | GEO
Project description:MAF1 represses Pol III-mediated transcription by interfering with TFIIIB and Pol III. Herein, we found that MAF1 knockdown induced CDKN1A transcription and chromatin looping concurrently with Pol III recruitment. Simultaneous knockdown of MAF1 with Pol III or BRF1 (subunit of TFIIIB) diminished the activation and looping effect, which indicates that recruiting Pol III was required for activation of Pol II-mediated transcription and chromatin looping. ChIP analysis after MAF1 knockdown indicated enhanced binding of Pol III and BRF1, as well as of CFP1, p300, and PCAF, which are factors that mediate active histone marks, along with the binding of TBP and POLR2E to the CDKN1A promoter. Simultaneous knockdown with Pol III abolished these regulatory events. Similar results were obtained for GDF15. Our results reveal a novel mechanism by which MAF1 and Pol III regulate the activity of a protein-coding gene transcribed by Pol II.
2015-06-10 | GSE42239 | GEO