Mapping nucleosome positions using DNase-seq

Genome Research
Jianling ZhongAlexander J Hartemink

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 l...Continue Reading

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Citations

Oct 20, 2018·Nucleic Acids Research·Yongbing ZhaoJingfa Xiao
Sep 22, 2017·Epigenetics & Chromatin·Ryohei NakamuraHiroyuki Takeda
Jul 17, 2018·Briefings in Bioinformatics·Yongjing LiuMing Chen
Nov 30, 2018·PLoS Genetics·Alexander J BrownSteven A Roberts
Aug 17, 2020·Epigenetics : Official Journal of the DNA Methylation Society·Anagh RayRonita Nag Chaudhuri
Apr 19, 2016·Epigenetics : Official Journal of the DNA Methylation Society·Wenjuan ZhangShaying Zhao
Feb 20, 2021·Nature Genetics·Žiga AvsecJulia Zeitlinger
Apr 10, 2018·Biophysical Journal·Răzvan V Chereji, David J Clark
Apr 21, 2020·Journal of Structural Biology·Romain RetureauBrigitte Hartmann

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