ArticleGenome biology2019
Quantitative MNase-seq accurately maps nucleosome occupancy levels.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
86 citing papers in PubMed, 150 citations in OpenAlex.
- ATAC-seq and MNase-seq Detect Distinct Modes of Chromatin Accessibility.bioRxiv : the preprint server for biology · 2026Article
- Satellite DNAs in Drosophila koepferae (repleta group) reveal patterns of origin, chromosomal organization, transcription, and turnover in the buzzatii cluster.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
- Chromatin accessibility classification of TAD boundaries discloses new architectural proteins.Nucleic acids research · 2026Article
- Genome-wide rotational and translational phasing of nucleosomes with human transcription factors.Molecular cell · 2026Article
- CAD-C: An engineered nuclease enables repair-freebioRxiv : the preprint server for biology · 2026Article
- ATP2B4 driven chromatin compaction exacerbates pancreatic cancer radiotherapy resistance.Cell death discovery · 2026Article
- An MNase-ChIP-Seq Protocol to Profile Histone Modifications at a DNA Break in Yeast.Methods and protocols · 2026Article
- Article
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- A Scalable MNase-seq Framework for Reproducible Nucleosome Profiling across Pluripotent Stem Cell and Cardiomyocyte Models.Computational and structural biotechnology journal · 2026Article
- Simulating cell-free chromatin using preclinical cancer models for liquid biopsy applications.iScience · 2025Article
- 3D chromatin structures precede genome activation in Drosophila embryogenesis.Cell genomics · 2025Article
- Quantitative single-cell imaging suggests increased global chromatin accessibility in tumor versus non-tumor cell lines.iScience · 2025Article
- Coordinated control of genome-nuclear lamina interactions by topoisomerase 2B and lamin B receptor.Nucleic acids research · 2025Article
- Article
- The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.PLoS computational biology · 2025Article
- Cold-induced nucleosome dynamics linked to silencing of Arabidopsis FLC.Nature communications · 2025Article
- HBV-driven host chromatin accessibility changes affect liver metabolic pathways, iron homeostasis and promote a preneoplastic phenotype.Journal of experimental & clinical cancer research : CR · 2025Article
- High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion.Nature communications · 2025Article
- Triplexes Color the Chromaverse by Modulating Nucleosome Phasing and Anchoring Chromatin Condensates.International journal of molecular sciences · 2025Review
26 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Micrococcal nuclease (MNase) is widely used to map nucleosomes. However, its aggressive endo-/exo-nuclease activities make MNase-seq unreliable for determining nucleosome occupancies, because cleavages within linker regions produce oligo- and mono-nucleosomes, whereas cleavages within nucleosomes destroy them. Here, we introduce a theoretical framework for predicting nucleosome occupancies and an experimental protocol with appropriate spike-in normalization that confirms our theory and provides accurate occupancy levels over an MNase digestion time course. As with human cells, we observe no overall differences in nucleosome occupancies between Drosophila euchromatin and heterochromatin, which implies that heterochromatic compaction does not reduce MNase accessibility of linker DNA.
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Registered trials
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.