Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping

Cell. 2016 Dec 1;167(6):1555-1570.e15. doi: 10.1016/j.cell.2016.10.049. Epub 2016 Nov 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. We uncovered surprising 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 nucleosomes occupy DNA targets for a subset of DNA-binding proteins, including CCCTC-binding factor (CTCF) and pluripotency factors. Furthermore, we provide 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. Taken together, we establish an accurate method for defining the nucleosome landscape and provide a valuable resource for studying nucleosome-mediated gene regulation in mammalian cells.

Keywords: CTCF; MNase; chemical biology; chromatin; embryonic stem cells; epigenetics; nucleosomes; pioneer transcription factors; pluripotency; splicing.

MeSH terms

  • Animals
  • CCCTC-Binding Factor
  • Genome-Wide Association Study
  • Mice
  • Mouse Embryonic Stem Cells / metabolism*
  • Nucleosomes / genetics*
  • RNA Polymerase II / metabolism
  • RNA Splice Sites
  • RNA Splicing
  • Repressor Proteins / metabolism
  • Saccharomyces cerevisiae / genetics
  • Transcription Initiation Site
  • Transcription, Genetic


  • CCCTC-Binding Factor
  • Ctcf protein, mouse
  • Nucleosomes
  • RNA Splice Sites
  • Repressor Proteins
  • RNA Polymerase II