title: Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome.
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.
authors.affiliation: Laboratory of Pathology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Fedor
authors.initials: F
authors.lastname: Kouzine
authors.affiliation: National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: Damian
authors.initials: D
authors.lastname: Wojtowicz
authors.affiliation: Laboratory of Pathology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Laura
authors.initials: L
authors.lastname: Baranello
authors.affiliation: Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Arito
authors.initials: A
authors.lastname: Yamane
authors.affiliation: Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Steevenson
authors.initials: S
authors.lastname: Nelson
authors.affiliation: Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Resch
authors.affiliation: Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Kyong-Rim
authors.initials: KR
authors.lastname: Kieffer-Kwon
authors.affiliation: UC Davis Genome Center, University of California Davis, Davis, CA 95616, USA.
authors.forename: Craig J
authors.initials: CJ
authors.lastname: Benham
authors.affiliation: Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Rafael
authors.initials: R
authors.lastname: Casellas
authors.affiliation: National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA. Electronic address: przytyck@ncbi.nlm.nih.gov.
authors.forename: Teresa M
authors.initials: TM
authors.lastname: Przytycka
authors.affiliation: Laboratory of Pathology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: levens@helix.nih.gov.
authors.forename: David
authors.initials: D
authors.lastname: Levens
mesh_terms: D000818:Animals; D002843:Chromatin; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D018983:DNA Footprinting / Q000379:methods*; D004277:DNA, Single-Stranded / Q000648:ultrastructure; D005656:Fungal Proteins; D054856:G-Quadruplexes; D005786:Gene Expression Regulation / Q000502:physiology; D016678:Genome; D008322:Mammals / Q000235:genetics; D017895:Manganese Compounds / Q000378:metabolism; D051379:Mice; D009690:Nucleic Acid Conformation; D009707:Nucleosomes; D010087:Oxides / Q000378:metabolism; D011485:Protein Binding; D015719:Single-Strand Specific DNA and RNA Endonucleases
chemical_list: D002843:Chromatin; D004277:DNA, Single-Stranded; D005656:Fungal Proteins; D017895:Manganese Compounds; D009707:Nucleosomes; D010087:Oxides; C048856:permanganic acid; D004247:DNA; C526098:Endonuclease S1, Aspergillus; D015719:Single-Strand Specific DNA and RNA Endonucleases
keywords: DNA topology; H-DNA; SIDD; Z-DNA; chromatin; cruciform; non-B DNA; quadruplex; supercoiling; transcription