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Genome Biol. 2018 Feb 9;19(1):19. doi: 10.1186/s13059-018-1398-0.

Precise genome-wide mapping of single nucleosomes and linkers in vivo.

Author information

1
Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
2
Howard Hughes Medical Institute and Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
3
Howard Hughes Medical Institute and Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA. steveh@fhcrc.org.

Abstract

We developed a chemical cleavage method that releases single nucleosome dyad-containing fragments, allowing us to precisely map both single nucleosomes and linkers with high accuracy genome-wide in yeast. Our single nucleosome positioning data reveal that nucleosomes occupy preferred positions that differ by integral multiples of the DNA helical repeat. By comparing nucleosome dyad positioning maps to existing genomic and transcriptomic data, we evaluated the contributions of sequence, transcription, and histones H1 and H2A.Z in defining the chromatin landscape. We present a biophysical model that neglects DNA sequence and shows that steric occlusion suffices to explain the salient features of nucleosome positioning.

KEYWORDS:

Biophysical modeling; Chemical cleavage mapping; Linker quantization

PMID:
29426353
PMCID:
PMC5807854
DOI:
10.1186/s13059-018-1398-0
[Indexed for MEDLINE]
Free PMC Article

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