Combinations of histone modifications mark exon inclusion levels
2012 (English)In: PLoS ONE, ISSN 1932-6203, Vol. 7, no 1, e29911Article in journal (Refereed) Published
Splicing is a complex process regulated by sequence at the classical splice sites and other motifs in exons and introns with an enhancing or silencing effect. In addition, specific histone modifications on nucleosomes positioned over the exons have been shown to correlate both positively and negatively with exon expression. Here, we trained a model of "IF … THEN …" rules to predict exon inclusion levels in a transcript from histone modification patterns. Furthermore, we showed that combinations of histone modifications, in particular those residing on nucleosomes preceding or succeeding the exon, are better predictors of exon inclusion levels than single modifications. The resulting model was evaluated with cross validation and had an average accuracy of 72% for 27% of the exons, which demonstrates that epigenetic signals substantially mark alternative splicing.
Place, publisher, year, edition, pages
2012. Vol. 7, no 1, e29911
Cell and Molecular Biology
IdentifiersURN: urn:nbn:se:uu:diva-175875DOI: 10.1371/journal.pone.0029911ISI: 000312662100045PubMedID: 22242188OAI: oai:DiVA.org:uu-175875DiVA: diva2:533278
FunderKnut and Alice Wallenberg FoundationSwedish Foundation for Strategic Research Swedish Research CouncilSwedish Cancer Society