ArticleGenome research2011
High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- The role of transcript regions and amino acid choice in nucleosome positioning.NAR genomics and bioinformatics · 2023Article
- Topoisomerases I and II facilitate condensin DC translocation to organize and repress X chromosomes in C. elegans.Molecular cell · 2022Article
- Article
- Genomes of Multicellular Organisms Have Evolved to Attract Nucleosomes to Promoter Regions.Biophysical journal · 2017Article
- Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans.Genome research · 2017Article
- The time-resolved transcriptome of C. elegans.Genome research · 2016Article
- Fine-Scale Crossover Rate Variation on the Caenorhabditis elegans X Chromosome.G3 (Bethesda, Md.) · 2016Article
- An H4K16 histone acetyltransferase mediates decondensation of the X chromosome inEpigenetics & chromatin · 2016Article
- Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.PLoS computational biology · 2015Article
- Mechanisms of x chromosome dosage compensation.Journal of genomics · 2015Review
- Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells.PloS one · 2015Article
- Linking dosage compensation and X chromosome nuclear organization in C. elegans.Nucleus (Austin, Tex.) · 2015Article
- BRG1/SMARCA4 inactivation promotes non-small cell lung cancer aggressiveness by altering chromatin organization.Cancer research · 2014Article
- Regulation of the X chromosomes in Caenorhabditis elegans.Cold Spring Harbor perspectives in biology · 2014Review
- pENCODE: a plant encyclopedia of DNA elements.Annual review of genetics · 2014Review
- Article
- Transcriptional regulation of gene expression in C. elegans.WormBook : the online review of C. elegans biology · 2013Review
- Global remodeling of nucleosome positions in C. elegans.BMC genomics · 2013Article
- Genome-wide analysis of condensin binding in Caenorhabditis elegans.Genome biology · 2013Article
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4 authors.
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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.
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