title: Mapping nucleosome positions using DNase-seq.
abstract: Although deoxyribonuclease I (DNase I) was used to probe the structure of the nucleosome in the 1960s and 1970s, in the current high-throughput sequencing era, DNase I has mainly been used to study genomic regions devoid of nucleosomes. Here, we reveal for the first time that DNase I can be used to precisely map the (translational) positions of in vivo nucleosomes genome-wide. Specifically, exploiting a distinctive DNase I cleavage profile within nucleosome-associated DNA--including a signature 10.3 base pair oscillation that corresponds to accessibility of the minor groove as DNA winds around the nucleosome--we develop a Bayes-factor-based method that can be used to map nucleosome positions along the genome. Compared to methods that require genetically modified histones, our DNase-based approach is easily applied in any organism, which we demonstrate by producing maps in yeast and human. Compared to micrococcal nuclease (MNase)-based methods that map nucleosomes based on cuts in linker regions, we utilize DNase I cuts both outside and within nucleosomal DNA; the oscillatory nature of the DNase I cleavage profile within nucleosomal DNA enables us to identify translational positioning details not apparent in MNase digestion of linker DNA. Because the oscillatory pattern corresponds to nucleosome rotational positioning, it also reveals the rotational context of transcription factor (TF) binding sites. We show that potential binding sites within nucleosome-associated DNA are often centered preferentially on an exposed major or minor groove. This preferential localization may modulate TF interaction with nucleosome-associated DNA as TFs search for binding sites.
authors.affiliation: Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA; Department of Computer Science, Duke University, Durham, North Carolina 27708, USA;
authors.forename: Jianling
authors.initials: J
authors.lastname: Zhong
authors.affiliation: Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA; Department of Computer Science, Duke University, Durham, North Carolina 27708, USA;
authors.forename: Kaixuan
authors.initials: K
authors.lastname: Luo
authors.affiliation: Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708, USA; Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27708, USA;
authors.forename: Peter S
authors.initials: PS
authors.lastname: Winter
authors.affiliation: Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA; Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708, USA; Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA;
authors.forename: Gregory E
authors.initials: GE
authors.lastname: Crawford
authors.affiliation: Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA; Department of Statistical Science, Duke University, Durham, North Carolina 27708, USA.
authors.forename: Edwin S
authors.initials: ES
authors.lastname: Iversen
authors.affiliation: Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA; Department of Computer Science, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; Department of Statistical Science, Duke University, Durham, North Carolina 27708, USA.
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Hartemink
mesh_terms: D001665:Binding Sites; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000235:genetics* / Q000378:metabolism*; D003850:Deoxyribonuclease I / Q000378:metabolism*; D016681:Genome, Fungal; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009707:Nucleosomes / Q000378:metabolism*; D059372:Nucleotide Motifs; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D014157:Transcription Factors; D004247:DNA; D003850:Deoxyribonuclease I