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GenomicsRNA polymerase II pausing downstream of core histone genes is different from genes producing polyadenylated transcripts
Recent genome-wide chromatin immunoprecipitation coupled high throughput sequencing (ChIP-seq) analyses performed in various eukaryotic organisms, analysed RNA Polymerase II (Pol II) pausing around the transcription start sites of genes. In this study we have further investigated genome-wide binding...
ORGANISM(S): Homo sapiens 
2012-06-15 | E-GEOD-34001 | biostudies-arrayexpress
TranscriptomicsMitotic Transcriptional Clearance of Actively Engaged Pol II Through Transcriptional Elongation Control
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, ...
ORGANISM(S): Homo sapiens 
2015-10-30 | E-GEOD-71848 | biostudies-arrayexpress
GenomicsTyrosine phosphorylation of RNA Polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells
In mammals, the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II consists of 52 conserved heptapeptide repeats containing the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Post-translational modifications of the CTD coordinate the transcription cycle and various steps of mRNA matura...
ORGANISM(S): Homo sapiens 
2014-06-01 | E-GEOD-52914 | biostudies-arrayexpress
GenomicsBromodomain-Containing-Protein 4 (BRD4) Regulates RNA Polymerase II Serine 2 Phosphorylation in Human CD4+ T Cells
Transcriptional elongation by RNA polymerase II (Pol II) is regulated by positive transcription elongation factor b (P-TEFb) in association with Bromodomain-containing protein 4 (BRD4). We used genome-wide chromatin immunoprecipitation sequencing in primary human CD4+ T cells to reveal that BRD4 co-...
ORGANISM(S): Homo sapiens 
2012-11-14 | E-GEOD-33281 | biostudies-arrayexpress
GenomicsRapid transcription of arc/arg3.1 and other very fast immediate early genes in response to neuronal activity is mediated by a stalled RNA polymerase II mechanism
Transcription of immediate early genes (IEGs) in neurons is exquisitely sensitive to neuronal activity, but the mechanism underlying the earliest of these transcription events is largely unknown. Here we demonstrate that very fast IEGs (VF-IEGs) such as arc/arg3.1 are poised for rapid transcription ...
ORGANISM(S): Rattus norvegicus 
2011-05-24 | E-GEOD-22878 | biostudies-arrayexpress
GenomicsUVB induces a major genome-wide rearrangement of RNA polymerase II at transcribed human genes
Abstract Background: Faithful transcription of DNA is constantly threatened by different endogenous and environmental genotoxic effects. Transcription coupled repair has been described to quickly remove DNA lesions from the transcribed strand of active genes, permitting rapid resumption of blocked ...
ORGANISM(S): Homo sapiens 
2014-07-25 | E-GEOD-52789 | biostudies-arrayexpress
GenomicsPromoter proximal pausing and its regulation by c-Myc in embryonic stem cells: ChIP-Seq
Recruitment of the RNA Polymerase II (Pol II) transcription initiation apparatus to promoters by specific DNA binding transcription factors is well recognized as a key regulatory step in gene expression. We describe here evidence that promoter-proximal pausing is a general feature of transcription ...
ORGANISM(S): Mus musculus 
2010-04-02 | E-GEOD-20530 | biostudies-arrayexpress
TranscriptomicsA large fraction of extragenic RNA Pol II transcription sites overlap enhancers
Mammalian genomes are pervasively transcribed outside mapped protein-coding genes. One class of extragenic transcription products is represented by long non-coding RNAs (lncRNAs), some of which result from Pol_II transcription of bona-fide RNA genes. Whether all lncRNAs described insofar are product...
ORGANISM(S): Mus musculus 
2010-05-21 | E-GEOD-20370 | biostudies-arrayexpress
TranscriptomicsDetection of Pol IV-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis
24 nucleotide siRNAs are central players in RNA-directed DNA methylation (RdDM), a process that establishes DNA methylation at transposable elements to ensure genome stability. The plant-specific RNA polymerase IV (Pol IV) is required for siRNA biogenesis and is thought to transcribe RdDM loci to pr...
ORGANISM(S): Arabidopsis thaliana 
2014-11-11 | E-GEOD-57215 | biostudies-arrayexpress
TranscriptomicsNET-seq of S. cerevisiae cells after knocking-out genes encoding various mRNA decay factors
NET-seq was performed on yeast strains carrying deletions of mRNA decay factors (plus a control) in order to assess the effect of their deletion on RNA polymerase II occupancy at genetic loci. This is in pursuit of understanding the process of mRNA buffering which links mRNA synthesis and decay.
ORGANISM(S): Saccharomyces cerevisiae 
2020-02-08 | E-MTAB-8749 | biostudies-arrayexpress
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