Document Detail


The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures.
MedLine Citation:
PMID:  23550086     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
RNA polymerase transcription initiation sites are largely unknown in Caenorhabditis elegans. The initial 5' end of most protein-coding transcripts is removed by trans-splicing, and noncoding initiation sites have not been investigated. We characterized the landscape of RNA Pol II transcription initiation, identifying 73,500 distinct clusters of initiation. Bidirectional transcription is frequent, with a peak of transcriptional pairing at 120 bp. We assign transcription initiation sites to 7691 protein-coding genes and find that they display features typical of eukaryotic promoters. Strikingly, the majority of initiation events occur in regions with enhancer-like chromatin signatures. Based on the overlap of transcription initiation clusters with mapped transcription factor binding sites, we define 2361 transcribed intergenic enhancers. Remarkably, productive transcription elongation across these enhancers is predominantly in the same orientation as that of the nearest downstream gene. Directed elongation from an upstream enhancer toward a downstream gene could potentially deliver RNA polymerase II to a proximal promoter, or alternatively might function directly as a distal promoter. Our results provide a new resource to investigate transcription regulation in metazoans.
Authors:
Ron A-J Chen; Thomas A Down; Przemyslaw Stempor; Q Brent Chen; Thea A Egelhofer; LaDeana W Hillier; Tess E Jeffers; Julie Ahringer
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't     Date:  2013-04-02
Journal Detail:
Title:  Genome research     Volume:  23     ISSN:  1549-5469     ISO Abbreviation:  Genome Res.     Publication Date:  2013 Aug 
Date Detail:
Created Date:  2013-08-02     Completed Date:  2014-02-19     Revised Date:  2014-06-10    
Medline Journal Info:
Nlm Unique ID:  9518021     Medline TA:  Genome Res     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1339-47     Citation Subset:  IM    
Data Bank Information
Bank Name/Acc. No.:
GEO/GSE42819
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MeSH Terms
Descriptor/Qualifier:
Animals
Caenorhabditis elegans / genetics*,  metabolism
Caenorhabditis elegans Proteins / metabolism*
Chromatin / genetics
Enhancer Elements, Genetic*
Molecular Sequence Annotation
Promoter Regions, Genetic*
RNA Polymerase II / metabolism*
Sequence Analysis, DNA
Transcription Initiation Site
Transcriptional Activation
Grant Support
ID/Acronym/Agency:
054523//Wellcome Trust; 092096//Wellcome Trust; 1-U01-HG004270-01/HG/NHGRI NIH HHS; //Cancer Research UK
Chemical
Reg. No./Substance:
0/Caenorhabditis elegans Proteins; 0/Chromatin; EC 2.7.7.-/RNA Polymerase II
Comments/Corrections

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