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

Citations Over Time

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.

Related Papers

• → RNA sequencing shows no dosage compensation of the active X-chromosome(2010)216 cited
• → Dosage compensation in flies and worms: the ups and downs of X-chromosome regulation(1998)114 cited
• → Dosage compensation and gene expression on the mammalian X chromosome: one plus one does not always equal two(2009)75 cited
• → An evolutionary consequence of dosage compensation on Drosophila melanogaster female X-chromatin structure?(2010)42 cited
• → Dosage compensation of the X chromosome and Turner syndrome(2006)4 cited