The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures
- RON A.-J. CHEN1,
- Thomas A. Down1,
- Przemyslaw Stempor1,
- Q. Brent Chen2,
- Thea A. Egelhofer3,
- LaDeana W. Hillier4,
- Tess E. Jeffers2 and
- Julie Ahringer5,6
- 1 The Gurdon Institute, University of Cambridge;
- 2 Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer Cent;
- 3 University of California Santa Cruz;
- 4 Washington University School of Medicine;
- 5 The Gurdon Institute and University of Cambridge
- ↵* Corresponding author; email: ja219{at}cam.ac.uk
Abstract
RNA polymerase transcription initiation sites are largely unknown in C. elegans. The initial 5' end of most protein-coding transcripts are removed by trans-splicing, and non-coding 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 towards 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.
- Received December 13, 2012.
- Accepted March 29, 2013.
- © 2013, Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
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