Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential Across a Mammalian Genome

Overview

Journal Cell Syst

Publisher Cell Press

Specialties Biology
Cell Biology
Molecular Biology

Date 2017 Feb 27

PMID 28237796

Citations 115

Authors

Fedor Kouzine

Damian Wojtowicz

Laura Baranello

Arito Yamane

Steevenson Nelson

Wolfgang Resch

Kyong-Rim Kieffer-Kwon

Craig J Benham

Rafael Casellas

Teresa M Przytycka

David Levens

Affiliations

Soon will be listed here.

Abstract

DNA in cells is predominantly B-form double helix. Though certain DNA sequences in vitro may fold into other structures, such as triplex, left-handed Z form, or quadruplex DNA, the stability and prevalence of these structures in vivo are not known. Here, using computational analysis of sequence motifs, RNA polymerase II binding data, and genome-wide potassium permanganate-dependent nuclease footprinting data, we map thousands of putative non-B DNA sites at high resolution in mouse B cells. Computational analysis associates these non-B DNAs with particular structures and indicates that they form at locations compatible with an involvement in gene regulation. Further analyses support the notion that non-B DNA structure formation influences the occupancy and positioning of nucleosomes in chromatin. These results suggest that non-B DNAs contribute to the control of a variety of critical cellular and organismal processes.

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