TY  - JOUR
A1  - Ercan, Sevinç
A1  - Lubling, Yaniv
A1  - Segal, Eran
A1  - Lieb, Jason D.
T1  - High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans
Y1  - 2011/02/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 237 
EP  - 244 
DO  - 10.1101/gr.115931.110 
VL  - 21 
IS  - 2 
UR  - http://genome.cshlp.org/content/21/2/237.abstract 
N2  - 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. 
ER  -