ArticleProceedings of the National Academy of Sciences of the United States of America2013
Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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68 citing papers in PubMed, 108 citations in OpenAlex.
- Differential nucleosome organization in human interphase and metaphase chromosomes.Molecular systems biology · 2026Article
- Contributions of DNA mechanics and trans-regulation to nucleosome positioning in Schizosaccharomyces pombe and its role in co-transcriptional splicing.Epigenetics & chromatin · 2026Article
- Nucleosome positioning shapes cryptic antisense transcription.PLoS genetics · 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
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- Chromatin higher-order folding as influenced by preferred values of linker DNA.Current opinion in structural biology · 2025Review
- Differential nucleosome organization in human interphase and metaphase chromosomes.bioRxiv : the preprint server for biology · 2025Article
- Nucleosome spacing can fine-tune higher-order chromatin assembly.Nature communications · 2025Article
- Consecutive low-frequency shifts in A/T content denote nucleosome positions across microeukaryotes.iScience · 2025Article
- Genome-Wide Nucleosome Mapping by H3Q85C-Directed Chemical Cleavage in Saccharomyces cerevisiae.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Physical modeling of nucleosome clustering in euchromatin resulting from interactions between epigenetic reader proteins.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Energy-driven genome regulation by ATP-dependent chromatin remodellers.Nature reviews. Molecular cell biology · 2024Review
- The structure of the NuA4-Tip60 complex reveals the mechanism and importance of long-range chromatin modification.Nature structural & molecular biology · 2023Article
- Sequence dependencies and mutation rates of localized mutational processes in cancer.Genome medicine · 2023Article
- An essential Noc3p dimerization cycle mediates ORC double-hexamer formation in replication licensing.Life science alliance · 2023Article
- Deciphering the mechanical code of the genome and epigenome.Nature structural & molecular biology · 2022Article
- Chromatin localization of nucleophosmin organizes ribosome biogenesis.Molecular cell · 2022Article
- Chromatin accessibility: methods, mechanisms, and biological insights.Nucleus (Austin, Tex.) · 2022Review
- In Vitro Mapping of Nucleosome Positions at Base-Pair Resolution Using Ortho-Phenanthroline.Current protocols · 2022Article
8 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
Abstract
Using a recently developed chemical approach, we have generated a genome-wide map of nucleosomes in vivo in Schizosaccharomyces pombe (S. pombe) at base pair resolution. The shorter linker length previously identified in S. pombe is due to a preponderance of nucleosomes separated by ∼4/5 bp, placing nucleosomes on opposite faces of the DNA. The periodic dinucleotide feature thought to position nucleosomes is equally strong in exons as in introns, demonstrating that nucleosome positioning information can be superimposed on coding information. Unlike the case in Saccharomyces cerevisiae, A/T-rich sequences are enriched in S. pombe nucleosomes, particularly at ±20 bp around the dyad. This difference in nucleosome binding preference gives rise to a major distinction downstream of the transcription start site, where nucleosome phasing is highly predictable by A/T frequency in S. pombe but not in S. cerevisiae, suggesting that the genomes and DNA binding preferences of nucleosomes have coevolved in different species. The poly (dA-dT) tracts affect but do not deplete nucleosomes in S. pombe, and they prefer special rotational positions within the nucleosome, with longer tracts enriched in the 10- to 30-bp region from the dyad. S. pombe does not have a well-defined nucleosome-depleted region immediately upstream of most transcription start sites; instead, the -1 nucleosome is positioned with the expected spacing relative to the +1 nucleosome, and its occupancy is negatively correlated with gene expression. Although there is generally very good agreement between nucleosome maps generated by chemical cleavage and micrococcal nuclease digestion, the chemical map shows consistently higher nucleosome occupancy on DNA with high A/T content.
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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.