Abstract
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.
Original language | English (US) |
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Pages (from-to) | 1555-1570.e15 |
Journal | Cell |
Volume | 167 |
Issue number | 6 |
DOIs | |
State | Published - Dec 1 2016 |
Keywords
- CTCF
- MNase
- chemical biology
- chromatin
- embryonic stem cells
- epigenetics
- nucleosomes
- pioneer transcription factors
- pluripotency
- splicing
ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)