ArticleJournal of molecular biology2012
Micrococcal nuclease does not substantially bias nucleosome mapping.
Article in Journal of molecular biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed, 79 citations in OpenAlex.
- Two essential criteria for transcription factor footprint discovery using V-plot.Molecular systems biology · 2026Article
- CAD-C: An engineered nuclease enables repair-freebioRxiv : the preprint server for biology · 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
- FENGC: Targeted, Multiplexed, and Integrated Single-Molecule Profiling of Chromatin Accessibility and DNA Methylation.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Interrogating the regulatory epigenome of cellular senescence.Cellular and molecular life sciences : CMLS · 2025Review
- Chromatin architecture mapping by multiplex proximity tagging.Molecular cell · 2025Article
- Coupling of an Au@AgPt nanozyme array with an micrococcal nuclease-specific responsiveness strategy for colorimetric/SERS sensing ofJournal of pharmaceutical analysis · 2025Article
- MNase-seq to Identify Genome-Wide DNA-Protein Interactions.Methods in molecular biology (Clifton, N.J.) · 2025Article
- New Perspectives on the Importance of Cell-Free DNA Biology.Diagnostics (Basel, Switzerland) · 2022Review
- Cell-Free DNA Fragmentation Patterns in a Cancer Cell Line.Diagnostics (Basel, Switzerland) · 2022Article
- Aberrant nucleosome organization in mouse SCNT embryos revealed by ULI-MNase-seq.Stem cell reports · 2022Article
- nMOWChIP-seq: low-input genome-wide mapping of non-histone targets.NAR genomics and bioinformatics · 2022Article
- GC content strongly influences the role of poly(dA) in the intrinsic nucleosome positioning in Saccharomyces cerevisiae.Yeast (Chichester, England) · 2022Article
- The macro and micro of chromosome conformation capture.Wiley interdisciplinary reviews. Developmental biology · 2021Review
- The native cistrome and sequence motif families of the maize ear.PLoS genetics · 2021Article
- Characterizing Genetic Regulatory Elements in Ovine Tissues.Frontiers in genetics · 2021Article
- Translational Opportunities for Microfluidic Technologies to Enable Precision Epigenomics.Analytical chemistry · 2020Article
- Genomic methods in profiling DNA accessibility and factor localization.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2020Article
- Biased visibility in Hi-C datasets marks dynamically regulated condensed and decondensed chromatin states genome-wide.BMC genomics · 2020Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
We have mapped sequence-directed nucleosome positioning on genomic DNA molecules using high-throughput sequencing. Chromatins, prepared by reconstitution with either chicken or frog histones, were separately digested to mononucleosomes using either micrococcal nuclease (MNase) or caspase-activated DNase (CAD). Both enzymes preferentially cleave internucleosomal (linker) DNA, although they do so by markedly different mechanisms. MNase has hitherto been very widely used to map nucleosomes, although concerns have been raised over its potential to introduce bias. Having identified the locations and quantified the strength of both the chicken or frog histone octamer binding sites on each DNA, the results obtained with the two enzymes were compared using a variety of criteria. Both enzymes displayed sequence specificity in their preferred cleavage sites, although the nature of this selectivity was distinct for the two enzymes. In addition, nucleosomes produced by CAD nuclease are 8-10 bp longer than those produced with MNase, with the CAD cleavage sites tending to be 4-5 bp further out from the nucleosomal dyad than the corresponding MNase cleavage sites. Despite these notable differences in cleavage behaviour, the two nucleases identified essentially equivalent patterns of nucleosome positioning sites on each of the DNAs tested, an observation that was independent of the histone type. These results indicate that biases in nucleosome positioning data collected using MNase are, under our conditions, not significant.
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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.