ArticleGenome research2016
Mapping nucleosome positions using DNase-seq.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Genome-wide rotational and translational phasing of nucleosomes with human transcription factors.Molecular cell · 2026Article
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model.Genome biology · 2026Article
- Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation.Genome research · 2026Article
- Chromatin-dependent motif syntax defines differentiation trajectories.Molecular cell · 2025Article
- Genome-wide maps of UV damage repair and mutation suppression by CPD photolyase.Nucleic acids research · 2025Article
- Inferring differential protein binding from time-series chromatin accessibility data.Bioinformatics advances · 2025Article
- ATAC-seq exposes differences in chromatin accessibility leading to distinct leaf shapes in mulberry.Plant direct · 2022Article
- DeepNup: Prediction of Nucleosome Positioning from DNA Sequences Using Deep Neural Network.Genes · 2022Article
- Review
- Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data.Genome research · 2022Article
- Galaxy Dnpatterntools for Computational Analysis of Nucleosome Positioning Sequence Patterns.International journal of molecular sciences · 2022Article
- Article
- Deacetylation of H4 lysine16 affects acetylation of lysine residues in histone H3 and H4 and promotes transcription of constitutive genes.Epigenetics · 2021Article
- Base-resolution models of transcription-factor binding reveal soft motif syntax.Nature genetics · 2021Article
- Chromatin accessibility profiling methods.Nature reviews. Methods primers · 2021Article
- Plasma DNA Profile Associated with DNASE1L3 Gene Mutations: Clinical Observations, Relationships to Nuclease Substrate Preference, and In Vivo Correction.American journal of human genetics · 2020Article
- RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy.Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- ) · 2020Article
- Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana.Genome biology · 2020Article
- Asymmetric repair of UV damage in nucleosomes imposes a DNA strand polarity on somatic mutations in skin cancer.Genome research · 2020Article
Corrections and comments
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Authors and funding
6 authors.
Funding
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.
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