ArticleGenome research2015
Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 240 papers.
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Who cites it
240 citing papers in PubMed.
- ATAC-seq and MNase-seq Detect Distinct Modes of Chromatin Accessibility.bioRxiv : the preprint server for biology · 2026Article
- Two essential criteria for transcription factor footprint discovery using V-plot.Molecular systems biology · 2026Article
- Multi-Omics Dissection and Functional Validation of Candidate Regulators Modulating Stress Tolerance and Xylose Utilization in the Natural Yeast Strain YB-2625.Journal of fungi (Basel, Switzerland) · 2026Article
- Deciphering global transcriptional dynamics coordinated by gene-gene regulatory interactions using single-cell data.Molecular systems biology · 2026Article
- Genome-wide rotational and translational phasing of nucleosomes with human transcription factors.Molecular cell · 2026Article
- On the state of chromatin in mammalian sperm.bioRxiv : the preprint server for biology · 2026Article
- Distinct associations of pioneer factor Ascl1-E12a with nucleosomes drive changes in cell fate.Molecular cell · 2026Article
- Chromatin accessibility dynamics and transcriptional regulation in Tetrahymena thermophila.Science China. Life sciences · 2026Article
- Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq.Nature communications · 2026Article
- Beyond chromatin accessibility: bulk ATAC-seq as an integrative assay to portray genomes and epigenomes.NAR genomics and bioinformatics · 2026Article
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- TBP regulates transposable element expression in early mouse embryos.The EMBO journal · 2026Article
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- Anhydrobiosis as a Model of Aging and Longevity: The Role of Autophagy and Metabolism in Yeast Cells.Microbial ecology · 2026Review
- Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs.Nature neuroscience · 2026Article
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- Sequence bias in chromatin fragmentation leads to misinterpretation of protein-DNA interactions in vivo.Genome biology · 2026Article
- Article
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- Deciphering the 3D genome organization across species from Hi-C data.Nucleic acids research · 2026Article
180 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
Transcription factors canonically bind nucleosome-free DNA, making the positioning of nucleosomes within regulatory regions crucial to the regulation of gene expression. Using the assay of transposase accessible chromatin (ATAC-seq), we observe a highly structured pattern of DNA fragment lengths and positions around nucleosomes in Saccharomyces cerevisiae, and use this distinctive two-dimensional nucleosomal "fingerprint" as the basis for a new nucleosome-positioning algorithm called NucleoATAC. We show that NucleoATAC can identify the rotational and translational positions of nucleosomes with up to base-pair resolution and provide quantitative measures of nucleosome occupancy in S. cerevisiae, Schizosaccharomyces pombe, and human cells. We demonstrate the application of NucleoATAC to a number of outstanding problems in chromatin biology, including analysis of sequence features underlying nucleosome positioning, promoter chromatin architecture across species, identification of transient changes in nucleosome occupancy and positioning during a dynamic cellular response, and integrated analysis of nucleosome occupancy and transcription factor binding.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.