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Cell Syst. 2017 Mar 22;4(3):344-356.e7. doi: 10.1016/j.cels.2017.01.013. Epub 2017 Feb 22.

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

Author information

1
Laboratory of Pathology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA.
2
National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA.
3
Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA.
4
UC Davis Genome Center, University of California Davis, Davis, CA 95616, USA.
5
National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA. Electronic address: przytyck@ncbi.nlm.nih.gov.
6
Laboratory of Pathology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: levens@helix.nih.gov.

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.

KEYWORDS:

DNA topology; H-DNA; SIDD; Z-DNA; chromatin; cruciform; non-B DNA; quadruplex; supercoiling; transcription

PMID:
28237796
DOI:
10.1016/j.cels.2017.01.013
[Indexed for MEDLINE]
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