Nucleosomes are well positioned in exons and carry characteristic histone modifications
- Robin Andersson1,4,
- Stefan Enroth1,4,
- Alvaro Rada-Iglesias1,4,
- Claes Wadelius2,5 and
- Jan Komorowski1,3,5
- 1 The Linnaeus Centre for Bioinformatics, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden;
- 2 Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-75185 Uppsala, Sweden;
- 3 Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, PL-02-106 Warszawa, Poland
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↵4 These authors contributed equally to this work.
Abstract
The genomes of higher organisms are packaged in nucleosomes with functional histone modifications. Until now, genome-wide nucleosome and histone modification studies have focused on transcription start sites (TSSs) where nucleosomes in RNA polymerase II (RNAPII) occupied genes are well positioned and have histone modifications that are characteristic of expression status. Using public data, we here show that there is a higher nucleosome-positioning signal in internal human exons and that this positioning is independent of expression. We observed a similarly strong nucleosome-positioning signal in internal exons of Caenorhabditis elegans. Among the 38 histone modifications analyzed in man, H3K36me3, H3K79me1, H2BK5me1, H3K27me1, H3K27me2, and H3K27me3 had evidently higher signals in internal exons than in the following introns and were clearly related to exon expression. These observations are suggestive of roles in splicing. Thus, exons are not only characterized by their coding capacity, but also by their nucleosome organization, which seems evolutionarily conserved since it is present in both primates and nematodes.
Footnotes
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↵5 Corresponding authors.
E-mail claes.wadelius{at}genpat.uu.se; fax +46-18-471-4808.
E-mail jan.komorowski{at}lcb.uu.se; fax +46-18-471-6698.
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[Supplemental material is available online at http://www.genome.org.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.092353.109.
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- Received February 6, 2009.
- Accepted June 19, 2009.
- Copyright © 2009 by Cold Spring Harbor Laboratory Press
