Chemical Mapping Reveals Novel Features of The Nucleosome Landscape in Mouse Embryonic Stem Cells 

  • Lilien N. Voong (Contributor)
  • Liqun Xi (Contributor)
  • Amy Sebeson (Contributor)
  • Bin Xiong (Contributor)
  • Jiping Wang (Contributor)
  • Xiaozhong Wang (Contributor)



Accession Number: GSE82127

GPL13112: Illumina HiSeq 2000 (Mus musculus)

Organism: Mus musculus

Published on 2016-11-23

Nucleosome organization influences gene activity by controlling DNA accessibility to transcription machinery. Here, we develop a chemical biology approach to determine mammalian nucleosome positions genome-wide. Using this strategy, we uncover surprising new features of nucleosome organization in mouse embryonic stem cells. In contrast to the prevailing model, we observe that for nearly all mouse genes a class of fragile nucleosomes occupies previously designated nucleosome-depleted regions around transcription start sites and transcription termination sites. We show that a subset of DNA-binding proteins including insulator CTCF and pluripotency factors co-occupy DNA targets with nucleosomes. Furthermore, we provide in vivo evidence that promoter-proximal nucleosomes, with the +1 nucleosome in particular, contribute to the pausing of RNA Polymerase II. Lastly, we find a characteristic preference for nucleosomes at exon-intron junctions. Altogether, we establish an accurate method for defining the nucleosome landscape, and provide a valuable resource for studying nucleosome-mediated gene regulation in mammalian cells.

Overall Design:
5 samples total. Chemical sample was analyzed with high throughput paired-end parallel sequencing. MNase samples were analyzed with high throughput paired-end parallel sequencing. 4 RNA samples from mouse ES cells (H4S47C Chemical vs WT) treated with 2i or Lif culture conditions.

Name: Liqun Xi
Organization: Northwestern University
Deparment: Statistics
Address: 2006 Sheridan Road Evanston IL 60208 USA

Organization: GEO
Address: USA
Date made availableJun 1 2016
PublisherGene Expression Omnibus

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