title: Nucleosome positioning as a determinant of exon recognition.
abstract: Chromatin structure influences transcription, but its role in subsequent RNA processing is unclear. Here we present analyses of high-throughput data that imply a relationship between nucleosome positioning and exon definition. First, we have found stable nucleosome occupancy within human and Caenorhabditis elegans exons that is stronger in exons with weak splice sites. Conversely, we have found that pseudoexons--intronic sequences that are not included in mRNAs but are flanked by strong splice sites--show nucleosome depletion. Second, the ratio between nucleosome occupancy within and upstream from the exons correlates with exon-inclusion levels. Third, nucleosomes are positioned central to exons rather than proximal to splice sites. These exonic nucleosomal patterns are also observed in non-expressed genes, suggesting that nucleosome marking of exons exists in the absence of transcription. Our analysis provides a framework that contributes to the understanding of splicing on the basis of chromatin architecture.
authors.affiliation: Center for Genomic Regulation, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
authors.forename: Hagen
authors.initials: H
authors.lastname: Tilgner
authors.forename: Christoforos
authors.initials: C
authors.lastname: Nikolaou
authors.forename: Sonja
authors.initials: S
authors.lastname: Althammer
authors.forename: Michael
authors.initials: M
authors.lastname: Sammeth
authors.forename: Miguel
authors.initials: M
authors.lastname: Beato
authors.forename: Juan
authors.initials: J
authors.lastname: Valcárcel
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigó
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D001482:Base Composition; D017173:Caenorhabditis elegans / Q000235:genetics*; D005091:Exons; D015870:Gene Expression; D006657:Histones / Q000378:metabolism; D006801:Humans; D007438:Introns; D009707:Nucleosomes / Q000378:metabolism; D022821:RNA Splice Sites; D022661:RNA, Untranslated; D014158:Transcription, Genetic
chemical_list: D006657:Histones; D009707:Nucleosomes; D022821:RNA Splice Sites; D022661:RNA, Untranslated
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