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Genome Res. 2015 Mar;25(3):381-90. doi: 10.1101/gr.182618.114. Epub 2014 Dec 9.

Asymmetric nucleosomes flank promoters in the budding yeast genome.

Author information

1
Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
2
Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

Abstract

Nucleosomes in active chromatin are dynamic, but whether they have distinct structural conformations is unknown. To identify nucleosomes with alternative structures genome-wide, we used H4S47C-anchored cleavage mapping, which revealed that 5% of budding yeast (Saccharomyces cerevisiae) nucleosome positions have asymmetric histone-DNA interactions. These asymmetric interactions are enriched at nucleosome positions that flank promoters. Micrococcal nuclease (MNase) sequence-based profiles of asymmetric nucleosome positions revealed a corresponding asymmetry in MNase protection near the dyad axis, suggesting that the loss of DNA contacts around H4S47 is accompanied by protection of the DNA from MNase. Chromatin immunoprecipitation mapping of selected nucleosome remodelers indicated that asymmetric nucleosomes are bound by the RSC chromatin remodeling complex, which is required for maintaining nucleosomes at asymmetric positions. These results imply that the asymmetric nucleosome-RSC complex is a metastable intermediate representing partial unwrapping and protection of nucleosomal DNA on one side of the dyad axis during chromatin remodeling.

PMID:
25491770
PMCID:
PMC4352886
DOI:
10.1101/gr.182618.114
[Indexed for MEDLINE]
Free PMC Article

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