| Citation | Ercan S, Lubling Y, Segal E, Lieb JD. High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans. Genome Res, 2011. |
| PubMed ID | 21177966 |
| Short Description | High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans. GEO Record: GSE20136 Platform: GPL8673 Download gene-centric, log2 transformed data: WBPaper00037949.ce.mr.csv |
| # of Conditions | 7 |
Full Description
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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. Experimental Details: WBPaper00037949:GermlineContaining_adult_rep1 WBPaper00037949:GermlineContaining_adult_rep2 WBPaper00037949:Germlineless_adult_rep1 WBPaper00037949:Germlineless_adult_rep2 WBPaper00037949:N2_embryo_rep1 WBPaper00037949:N2_embryo_rep2 WBPaper00037949:XO-hermaphrodite_L3_rep1. |
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