RNA content of transcription factories
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR655280.fastq.gz | Fastqsanger.gz | |||
| ERR655281.fastq.gz | Fastqsanger.gz | |||
| ERR655282.fastq.gz | Fastqsanger.gz | |||
| ERR655283.fastq.gz | Fastqsanger.gz | |||
| ERR655284.fastq.gz | Fastqsanger.gz |
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Project description:We have develop a simple fact method to isolate transcription factories and analyzed their RNA content as compared to total poly(A)+ and chromatin associated RNA fractions in presence or absence of pro-inflammatory cytokine.
2015-10-30 | E-MTAB-3020 | biostudies-arrayexpress
Project description:Transcription steps are marked by different modifications of the C-terminal domain of RNA polymerase II (RNAPII). Phosphorylation of Ser5 and Ser7 by cyclin-dependent kinase 7 (CDK7) as part of TFIIH marks initiation, whereas phosphorylation of Ser2 by CDK9 marks elongation. These processes are thought to take place in localized transcription foci in the nucleus, known as ‘‘transcription factories,’’ but it has been argued that the observed clusters/foci are mere fixation or labeling artifacts. We show that transcription factories exist in living cells as distinct foci by live-imaging fluorescently labeled CDK9, a kinase known to associate with active RNAPII. These foci were observed in different cell types derived from CDK9-mCherry knock-in mice. We show that these foci are very stable while highly dynamic in exchanging CDK9. Chromatin immunoprecipitation (ChIP) coupled with deep sequencing (ChIP-seq) data show that the genome-wide binding sites of CDK9 and initiating RNAPII overlap on transcribed genes. Immunostaining shows that CDK9- mCherry foci colocalize with RNAPII-Ser5P, much less with RNAPII-Ser2P, and not with CDK12 (a kinase reported to be involved in the Ser2 phosphorylation) or with splicing factor SC35. In conclusion, transcription factories exist in living cells, and initiation and elongation of transcripts takes place in different nuclear compartments.
2013-05-13 | GSE46849 | GEO
Project description:Transcription steps are marked by different modifications of the C-terminal domain of RNA polymerase II (RNAPII). Phosphorylation of Ser5 and Ser7 by cyclin-dependent kinase 7 (CDK7) as part of TFIIH marks initiation, whereas phosphorylation of Ser2 by CDK9 marks elongation. These processes are thought to take place in localized transcription foci in the nucleus, known as M-bM-^@M-^XM-bM-^@M-^Xtranscription factories,M-bM-^@M-^YM-bM-^@M-^Y but it has been argued that the observed clusters/foci are mere fixation or labeling artifacts. We show that transcription factories exist in living cells as distinct foci by live-imaging fluorescently labeled CDK9, a kinase known to associate with active RNAPII. These foci were observed in different cell types derived from CDK9-mCherry knock-in mice. We show that these foci are very stable while highly dynamic in exchanging CDK9. Chromatin immunoprecipitation (ChIP) coupled with deep sequencing (ChIP-seq) data show that the genome-wide binding sites of CDK9 and initiating RNAPII overlap on transcribed genes. Immunostaining shows that CDK9- mCherry foci colocalize with RNAPII-Ser5P, much less with RNAPII-Ser2P, and not with CDK12 (a kinase reported to be involved in the Ser2 phosphorylation) or with splicing factor SC35. In conclusion, transcription factories exist in living cells, and initiation and elongation of transcripts takes place in different nuclear compartments. Examination of genome occupancy of CDK9 and RNAPII that was performed by ChIP-seq in the MEL cell line as described (Soler et al. 2010, 2011) using CDK9 C20 antibody (Santa Cruz Biotechnology, C20, sc-484) and RNA Pol II antibody (Santa Cruz Biotechnology, N20, sc899),
2013-05-13 | E-GEOD-46849 | biostudies-arrayexpress
Project description:While mapping total and poly-adenylated human transcriptomes has now become routine, characterizing nascent transcripts remains challenging, largely because nascent RNAs have such short half-lives. Here, we describe a simple, fast and cost-effective method to isolate RNA associated with transcription factories, the sites responsible for the majority of nuclear transcription. Following stimulation of human endothelial cells with the pro-inflammatory cytokine TNFα, we isolate and analyse the RNA content of factories by sequencing. Comparison with total, poly(A)(+) and chromatin RNA fractions reveals that sequencing of purified factory RNA maps the complete nascent transcriptome; it is rich in intronic unprocessed transcript, as well as long intergenic non-coding (lincRNAs) and enhancer-associated RNAs (eRNAs), micro-RNA precursors and repeat-derived RNAs. Hence, we verify that transcription factories produce most nascent RNA and confer a regulatory role via their association with a set of specifically-retained non-coding transcripts.
| S-EPMC4538806 | biostudies-literature
Project description:Proteomic analysis of isolated viral factories along a timeline after infection of the amoeba Acanthamoeba polyphaga by the giant Mimivirus
2018-10-26 | PXD004203 | Pride
Project description:This SuperSeries is composed of the following subset Series: GSE38560: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (RNA-seq) GSE38561: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (ChIP-seq) GSE38562: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (genomic SEQ) GSE38563: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (MNase-seq) GSE38564: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (5) Refer to individual Series
2012-06-11 | E-GEOD-38577 | biostudies-arrayexpress
Project description:Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories
| PRJNA552868 | ENA
Project description:Polyploidization events are known to trigger extensive epigenetic and transcriptional alteration of the duplicated or merged genomes, accompanied by small- and large-scale conformational changes. The genome of modern hexaploid wheat (Triticum aestivum L.; 2n = 6x = 42) is the product of two rounds of interspecific hybridization between three closely related diploid species, resulting in the presence of distinct but highly syntenic sub-genomes (AA, BB and DD). We examined the large-scale chromatin architecture of the nucleus of wheat using Hi-C, a genome-wide chromatin conformation capture (3C) method and GISH, (genomic in situ hybridization). We found evidence that physical interactions occur with significantly higher frequency within sub genomes (A with A, B with B or D with D) than between sub genomes (A with B or D, etc. ...), defining sub-nuclear “genomic territories”. In addition, we observed a polarized distribution of facultative and constitutive heterochromatin that suggests a functional compartmentalization within the nucleus. On a local scale, we found that genes tend to interact mainly with other genes over long-distance “loops” that are especially established between genes presenting similar expression levels and bearing the same histone marks. Moreover, gene pairs in spatial proximity show similar changes in expression levels between shoots and roots. Consistently, we found that physical contact between genes is mediated by RNA polymerase II (RNAPII). Immunofluorescence assays with anti RNAP2 antibodies revealed the presence of “transcription factories” in which multiple interacting genes are co-transcribed. This indicates that local-scale topology is an important factor for transcriptional regulation as it determines the micro-compartimentalization of active genes within the nucleus.Our results provide a framework for understanding the physical organization of wheat genome and highlight the interplay between chromosome conformation and gene expression in wheat.
2020-03-02 | GSE133880 | GEO
Project description:Polyploidization events are known to trigger extensive epigenetic and transcriptional alteration of the duplicated or merged genomes, accompanied by small- and large-scale conformational changes. The genome of modern hexaploid wheat (Triticum aestivum L.; 2n = 6x = 42) is the product of two rounds of interspecific hybridization between three closely related diploid species, resulting in the presence of distinct but highly syntenic sub-genomes (AA, BB and DD). We examined the large-scale chromatin architecture of the nucleus of wheat using Hi-C, a genome-wide chromatin conformation capture (3C) method and GISH, (genomic in situ hybridization). We found evidence that physical interactions occur with significantly higher frequency within sub genomes (A with A, B with B or D with D) than between sub genomes (A with B or D, etc. ...), defining sub-nuclear “genomic territories”. In addition, we observed a polarized distribution of facultative and constitutive heterochromatin that suggests a functional compartmentalization within the nucleus. On a local scale, we found that genes tend to interact mainly with other genes over long-distance “loops” that are especially established between genes presenting similar expression levels and bearing the same histone marks. Moreover, gene pairs in spatial proximity show similar changes in expression levels between shoots and roots. Consistently, we found that physical contact between genes is mediated by RNA polymerase II (RNAPII). Immunofluorescence assays with anti RNAP2 antibodies revealed the presence of “transcription factories” in which multiple interacting genes are co-transcribed. This indicates that local-scale topology is an important factor for transcriptional regulation as it determines the micro-compartimentalization of active genes within the nucleus.Our results provide a framework for understanding the physical organization of wheat genome and highlight the interplay between chromosome conformation and gene expression in wheat.
2020-03-02 | GSE133879 | GEO
Project description:Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat_ChIP)
| PRJNA552870 | ENA