High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans
- Sevinç Ercan1,2,5,6,
- Yaniv Lubling3,5,
- Eran Segal3,4,6 and
- Jason D. Lieb1,2
- 1 Department of Biology, Carolina Center for the Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599-3280, USA;
- 2 Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-3280, USA;
- 3 Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel;
- 4 Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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↵5 These authors contributed equally to this work.
Abstract
We mapped nucleosome occupancy by paired-end Illumina sequencing in C. elegans embryonic cells, adult somatic cells, and a mix of adult somatic and germ cells. In all three samples, the nucleosome occupancy of gene promoters on the X chromosome differed from autosomal promoters. While both X and autosomal promoters exhibit a typical nucleosome-depleted region upstream of transcript start sites and a well-positioned +1 nucleosome, X-linked gene promoters on average exhibit higher nucleosome occupancy relative to autosomal promoters. We show that the difference between X and autosomes does not depend on the somatic dosage compensation machinery. Instead, the chromatin difference at promoters is partly encoded by DNA sequence, because a model trained on nucleosome sequence preferences from S. cerevisiae in vitro data recapitulate nearly completely the experimentally observed difference between X and autosomal promoters. The model predictions also correlate very well with experimentally determined occupancy values genome-wide. The nucleosome occupancy differences observed on X promoters may bear on mechanisms of X chromosome dosage compensation in the soma, and chromosome-wide repression of X in the germline.
Footnotes
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↵6 Corresponding authors.
E-mail ercan{at}email.unc.edu.
E-mail eran.segal{at}weizmann.ac.il.
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[Supplemental material is available for this article. The sequencing and microarray data from this study have been submitted to the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) under accession no. GSE20136.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.115931.110.
- Received September 27, 2010.
- Accepted November 15, 2010.
- Copyright © 2011 by Cold Spring Harbor Laboratory Press
