ReviewChromosoma2015
Nucleosome positioning in yeasts: methods, maps, and mechanisms.
Review in Chromosoma, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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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
30 citing papers in PubMed, 55 citations in OpenAlex.
- Context-dependent interplay of Swi-Snf and Tup1-Cyc8 influences chromatin and transcription at antagonistically regulated genes.Nature communications · 2026Article
- Variations in flanking or less conserved positions of Reb1 and Abf1 consensus binding sites lead to major changes in their ability to modulate nucleosome sliding activity.Biological research · 2025Article
- An integrated machine-learning model to predict nucleosome architecture.Nucleic acids research · 2024Article
- In silico design of DNA sequences for in vivo nucleosome positioning.Nucleic acids research · 2024Article
- Genome organization across scales: mechanistic insights from in vitro reconstitution studies.Biochemical Society transactions · 2024Review
- Dynamic nucleosome landscape elicits a noncanonical GATA2 pioneer model.Nature communications · 2022Article
- GC content strongly influences the role of poly(dA) in the intrinsic nucleosome positioning in Saccharomyces cerevisiae.Yeast (Chichester, England) · 2022Article
- Mammalian Micro-C-XL.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The Active Mechanism of Nucleosome Depletion by Poly(dA:dT) Tracts In Vivo.International journal of molecular sciences · 2021Review
- Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos.BMC bioinformatics · 2021Article
- Genome information processing by the INO80 chromatin remodeler positions nucleosomes.Nature communications · 2021Article
- Peculiarities ofInternational journal of molecular sciences · 2021Review
- Article
- Slow motions in A·T rich DNA sequence.Scientific reports · 2020Article
- [Identification of nucleosome positioning using support vector machine method based on comprehensive DNA sequence feature].Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi · 2020Article
- Beads on a string-nucleosome array arrangements and folding of the chromatin fiber.Nature structural & molecular biology · 2020Review
- Limited expression of non-integrating CpG-free plasmid is associated with increased nucleosome enrichment.PloS one · 2020Article
- Epigenome Regulation by Dynamic Nucleosome Unwrapping.Trends in biochemical sciences · 2020Review
- Absolute nucleosome occupancy map for theGenome research · 2019Article
- Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Eukaryotic nuclear DNA is packaged into nucleosomes. During the past decade, genome-wide nucleosome mapping across species revealed the high degree of order in nucleosome positioning. There is a conserved stereotypical nucleosome organization around transcription start sites (TSSs) with a nucleosome-depleted region (NDR) upstream of the TSS and a TSS-aligned regular array of evenly spaced nucleosomes downstream over the gene body. As nucleosomes largely impede access to DNA and thereby provide an important level of genome regulation, it is of general interest to understand the mechanisms generating nucleosome positioning and especially the stereotypical NDR-array pattern. We focus here on the most advanced models, unicellular yeasts, and review the progress in mapping nucleosomes and which nucleosome positioning mechanisms are discussed. There are four mechanistic aspects: How are NDRs generated? How are individual nucleosomes positioned, especially those flanking the NDRs? How are nucleosomes evenly spaced leading to regular arrays? How are regular arrays aligned at TSSs? The main candidates for nucleosome positioning determinants are intrinsic DNA binding preferences of the histone octamer, specific DNA binding factors, nucleosome remodeling enzymes, transcription, and statistical positioning. We summarize the state of the art in an integrative model where nucleosomes are positioned by a combination of all these candidate determinants. We highlight the predominance of active mechanisms involving nucleosome remodeling enzymes which may be recruited by DNA binding factors and the transcription machinery. While this mechanistic framework emerged clearly during recent years, the involved factors and their mechanisms are still poorly understood and require future efforts combining in vivo and in vitro approaches.
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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.