SPELL - Nematode - Dataset Details
New Search

Dataset Listing

Show Expression Levels

Download Expression Data

About the Website

SPELL Version 2.0.3

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 1316625150_help 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:
Tags 1316625150_help
Method: microarray, Species: Caenorhabditis elegans, Topic: gene expression - general