Categorical spectral analysis of periodicity in nucleosomal DNA

Nucleic Acids Research
Hu JinJun S Song

Abstract

DNA helical twist imposes geometric constraints on the location of histone-DNA interaction sites along nucleosomal DNA. Certain 10.5-bp periodic nucleotides in phase with these geometric constraints have been suggested to facilitate nucleosome positioning. However, the extent of nucleotide periodicity in nucleosomal DNA and its significance in directing nucleosome positioning still remain unclear. We clarify these issues by applying categorical spectral analysis to high-resolution nucleosome maps in two yeast species. We find that only a small fraction of nucleosomal sequences contain significant 10.5-bp periodicity. We further develop a spectral decomposition method to show that the previously observed periodicity in aligned nucleosomal sequences mainly results from proper phasing among nucleosomal sequences, and not from a preponderant occurrence of periodicity within individual sequences. Importantly, we show that this phasing may arise from the histones' proclivity for putting preferred nucleotides at some of the evenly spaced histone-DNA contact points with respect to the dyad axis. We demonstrate that 10.5-bp periodicity, when present, significantly facilitates rotational, but not translational, nucleosome positioning. Fi...Continue Reading

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Jul 18, 2016·Seminars in Immunology·Colin Logie, Hendrik G Stunnenberg
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Feb 5, 2021·Journal of Molecular Biology·Aakash BasuTaekjip Ha
Feb 20, 2021·Nature Genetics·Žiga AvsecJulia Zeitlinger

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