The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures

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...

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Bibliographic Details
Published in:Genome research 2013-08, Vol.23 (8), p.1339-1347
Main Authors: Chen, Ron A-J, Down, Thomas A, Stempor, Przemyslaw, Chen, Q Brent, Egelhofer, Thea A, Hillier, LaDeana W, Jeffers, Tess E, Ahringer, Julie
Format: Article
Language:English
Subjects:
Animals
Caenorhabditis elegans
Caenorhabditis elegans - genetics
Caenorhabditis elegans - metabolism
Caenorhabditis elegans Proteins - metabolism
Chromatin - genetics
Enhancer Elements, Genetic
Metazoa
Molecular Sequence Annotation
Promoter Regions, Genetic
Resource
RNA Polymerase II - metabolism
Sequence Analysis, DNA
Transcription Initiation Site
Transcriptional Activation
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Summary: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.
ISSN:1088-9051
1549-5469
DOI:10.1101/gr.153668.112