ArticleJournal of molecular biology2013
Combined micrococcal nuclease and exonuclease III digestion reveals precise positions of the nucleosome core/linker junctions: implications for high-resolution nucleosome mapping.
Article in Journal of molecular biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 27 citations in OpenAlex.
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- Single amino-acid differences define H2B variants and modify chromatin accessibility to induce EMT in breast cancer.Oncogene · 2026Article
- Sensitive effect of linker histone binding mode and subtype on chromatin condensation.Nucleic acids research · 2019Article
- Dynamics of Chromatin Fibers: Comparison of Monte Carlo Simulations with Force Spectroscopy.Biophysical journal · 2018Article
- Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA.Nature structural & molecular biology · 2017Article
- DNA topology in chromatin is defined by nucleosome spacing.Science advances · 2017Article
- Regulation of chromatin folding by conformational variations of nucleosome linker DNA.Nucleic acids research · 2017Article
- Article
- The proto-chromatosome: A fundamental subunit of chromatin?Nucleus (Austin, Tex.) · 2016Review
- The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences.Nucleic acids research · 2016Article
- Novel nucleosomal particles containing core histones and linker DNA but no histone H1.Nucleic acids research · 2016Article
- A brief review of nucleosome structure.FEBS letters · 2015Review
- Nucleosome positioning in yeasts: methods, maps, and mechanisms.Chromosoma · 2015Review
- Histone methyltransferases: novel targets for tumor and developmental defects.American journal of translational research · 2015Review
- Nucleosome-positioning sequence repeats impact chromatin silencing in yeast minichromosomes.Genetics · 2014Article
- nuMap: a web platform for accurate prediction of nucleosome positioning.Genomics, proteomics & bioinformatics · 2014Article
- Prediction of nucleosome rotational positioning in yeast and human genomes based on sequence-dependent DNA anisotropy.BMC bioinformatics · 2014Article
- Dynamic condensation of linker histone C-terminal domain regulates chromatin structure.Nucleic acids research · 2014Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Micrococcal nuclease (MNase) is extensively used in genome-wide mapping of nucleosomes but its preference for AT-rich DNA leads to errors in establishing precise positions of nucleosomes. Here, we show that the MNase digestion of nucleosomes assembled on a strong nucleosome positioning sequence, Widom's clone 601, releases nucleosome cores whose sizes are strongly affected by the linker DNA sequence. Our experiments produced nucleosomal DNA sizes varying between 147 and 155 bp, with positions of the MNase cuts reflecting positions of the A⋅T pairs rather than the nucleosome core/linker junctions determined by X-ray crystallography. Extent of chromatosomal DNA protection by linker histone H1 also depends on the linker DNA sequence. Remarkably, we found that a combined treatment with MNase and exonuclease III (exoIII) overcomes MNase sequence preference producing nucleosomal DNA trimmed symmetrically and precisely at the core/linker junctions regardless of the underlying DNA sequence. We propose that combined MNase/exoIII digestion can be applied to in situ chromatin for unbiased genome-wide mapping of nucleosome positions that is not influenced by DNA sequences at the core/linker junctions. The same approach can be also used for the precise mapping of the extent of linker DNA protection by H1 and other protein factors associated with nucleosome linkers.
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