ArticleMolecular cell2017
MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers.
Article in Molecular cell, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
What it found
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Who cites it
79 citing papers in PubMed, 140 citations in OpenAlex.
- RNA-independent cis-autoregulatory circuits within bidirectional gene pairs control metabolism.Science advances · 2026Article
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- Simulating cell-free chromatin using preclinical cancer models for liquid biopsy applications.iScience · 2025Article
- The ISW1 and CHD1 chromatin remodelers suppress global nucleosome dynamics in living yeast cells.Science advances · 2025Article
- SMAdd-seq: probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing.Nucleic acids research · 2025Article
- The histone chaperone Spn1 preserves chromatin protections at promoters and nucleosome positioning in open reading frames.G3 (Bethesda, Md.) · 2025Article
- SMAdd-seq: Probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing.bioRxiv : the preprint server for biology · 2025Article
- The yeast genome is globally accessible in living cells.Nature structural & molecular biology · 2025Article
- Size-based expectation maximization for characterizing nucleosome positions and subtypes.Genome research · 2024Article
- Transcriptional silencing in Saccharomyces cerevisiae: known unknowns.Epigenetics & chromatin · 2024Review
- In silico design of DNA sequences for in vivo nucleosome positioning.Nucleic acids research · 2024Article
- nucMACC: An MNase-seq pipeline to identify structurally altered nucleosomes in the genome.Science advances · 2024Article
- Targeting the chromatin structural changes of antitumor immunity.Journal of pharmaceutical analysis · 2024Review
- SEM: sized-based expectation maximization for characterizing nucleosome positions and subtypes.bioRxiv : the preprint server for biology · 2023Article
- Changes in adenoviral chromatin organization precede early gene activation upon infection.The EMBO journal · 2023Article
- The esBAF and ISWI nucleosome remodeling complexes influence occupancy of overlapping dinucleosomes and fragile nucleosomes in murine embryonic stem cells.BMC genomics · 2023Article
- Opposing Roles of FACT for Euchromatin and Heterochromatin in Yeast.Biomolecules · 2023Review
- Article
- Profiling Accessible Chromatin and Nucleosomes in the Mammalian Genome.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Chromatin accessibility: methods, mechanisms, and biological insights.Nucleus (Austin, Tex.) · 2022Review
19 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 commonly used to map nucleosomes genome-wide, but nucleosome maps are affected by the degree of digestion. It has been proposed that many yeast promoters are not nucleosome-free but instead occupied by easily digested, unstable, "fragile" nucleosomes. We analyzed the histone content of all MNase-sensitive complexes by MNase-ChIP-seq and sonication-ChIP-seq. We find that yeast promoters are predominantly bound by non-histone protein complexes, with little evidence for fragile nucleosomes. We do detect MNase-sensitive nucleosomes elsewhere in the genome, including at transcription termination sites. However, they have high A/T content, suggesting that MNase sensitivity does not indicate instability, but rather the preference of MNase for A/T-rich DNA, such that A/T-rich nucleosomes are digested faster than G/C-rich nucleosomes. We confirm our observations by analyzing ChIP-exo, chemical mapping, and ATAC-seq data from other laboratories. Thus, histone ChIP-seq experiments are essential to distinguish nucleosomes from other DNA-binding proteins that protect against MNase.
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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.