High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans

Sevinç Ercan, Yaniv Lubling, Eran Segal, Jason D. Lieb

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)237-244
Number of pages8
JournalGenome Research
Volume21
Issue number2
DOIs
StatePublished - Feb 1 2011

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ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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