title: The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures.
abstract: 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.affiliation: The Gurdon Institute, and Department of Genetics, University of Cambridge, Cambridge CB3 0DH, United Kingdom.
authors.forename: Ron A-J
authors.initials: RA
authors.lastname: Chen
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Down
authors.forename: Przemyslaw
authors.initials: P
authors.lastname: Stempor
authors.forename: Q Brent
authors.initials: QB
authors.lastname: Chen
authors.forename: Thea A
authors.initials: TA
authors.lastname: Egelhofer
authors.forename: LaDeana W
authors.initials: LW
authors.lastname: Hillier
authors.forename: Tess E
authors.initials: TE
authors.lastname: Jeffers
authors.forename: Julie
authors.initials: J
authors.lastname: Ahringer
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism; D029742:Caenorhabditis elegans Proteins / Q000378:metabolism*; D002843:Chromatin / Q000235:genetics; D004742:Enhancer Elements, Genetic; D058977:Molecular Sequence Annotation; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D024363:Transcription Initiation Site; D015533:Transcriptional Activation
chemical_list: D029742:Caenorhabditis elegans Proteins; D002843:Chromatin; D012319:RNA Polymerase II
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