ArticleGenome research2014
RSC-dependent constructive and destructive interference between opposing arrays of phased nucleosomes in yeast.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed, 93 citations in OpenAlex.
- Cohesin facilitates nucleosome invasion by transcription factors.Science advances · 2026Article
- Contributions of DNA mechanics and trans-regulation to nucleosome positioning in Schizosaccharomyces pombe and its role in co-transcriptional splicing.Epigenetics & chromatin · 2026Article
- TDG orchestrates ATF4-dependent gene transcription during retinoic acid-induced cell fate acquisition.Nucleic acids research · 2026Article
- Article
- Cohesin Facilitates Nucleosome Invasion by Transcription Factors.bioRxiv : the preprint server for biology · 2025Article
- The ISW1 and CHD1 chromatin remodelers suppress global nucleosome dynamics in living yeast cells.Science advances · 2025Article
- Regulation of DNA translocation of chromatin remodeler enzyme Chd1 by exit DNA unwrapping.Life metabolism · 2025Article
- The yeast genome is globally accessible in living cells.Nature structural & molecular biology · 2025Article
- Histone Acetyltransferases Gcn5 and Esa1 Regulate Occupancy of RSC to Maintain Nucleosome-Depleted Regions and Promote RSC Recruitment to Coding Regions Genome-Wide inMolecular and cellular biology · 2025Article
- Transcriptional silencing in Saccharomyces cerevisiae: known unknowns.Epigenetics & chromatin · 2024Review
- Examining chromatin heterogeneity through PacBio long-read sequencing of M.EcoGII methylated genomes: an m6A detection efficiency and calling bias correcting pipeline.Nucleic acids research · 2024Article
- Energy-driven genome regulation by ATP-dependent chromatin remodellers.Nature reviews. Molecular cell biology · 2024Review
- Genome-wide regulation of Pol II, FACT, and Spt6 occupancies by RSC in Saccharomyces cerevisiae.Gene · 2024Article
- A genome-wide comprehensive analysis of nucleosome positioning in yeast.PLoS computational biology · 2024Article
- Examining chromatin heterogeneity through PacBio long-read sequencing of M.EcoGII methylated genomes: an mbioRxiv : the preprint server for biology · 2023Article
- Yeast Heterochromatin Only Stably Silences Weak Regulatory Elements by Altering Burst Duration.bioRxiv : the preprint server for biology · 2023Article
- Differential requirements for Gcn5 and NuA4 HAT activities in the starvation-induced versus basal transcriptomes.Nucleic acids research · 2023Article
- The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site determination in Arabidopsis.Nucleic acids research · 2022Article
- Histone protein surface accessibility dictates direction of RSC-dependent nucleosome mobilization.Nucleic acids research · 2022Article
- RSC and GRFs confer promoter directionality by restricting divergent noncoding transcription.Life science alliance · 2022Article
6 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
RSC and SWI/SNF are related ATP-dependent chromatin remodeling machines that move nucleosomes, regulating access to DNA. We addressed their roles in nucleosome phasing relative to transcription start sites in yeast. SWI/SNF has no effect on phasing at the global level. In contrast, RSC depletion results in global nucleosome repositioning: Both upstream and downstream nucleosomal arrays shift toward the nucleosome-depleted region (NDR), with no change in spacing, resulting in a narrower and partly filled NDR. The global picture of RSC-depleted chromatin represents the average of a range of chromatin structures, with most genes showing a shift of the +1 or the -1 nucleosome into the NDR. Using RSC ChIP data reported by others, we show that RSC occupancy is highest on the coding regions of heavily transcribed genes, though not at their NDRs. We propose that RSC has a role in restoring chromatin structure after transcription. Analysis of gene pairs in different orientations demonstrates that phasing patterns reflect competition between phasing signals emanating from neighboring NDRs. These signals may be in phase, resulting in constructive interference and a regular array, or out of phase, resulting in destructive interference and fuzzy positioning. We propose a modified barrier model, in which a stable complex located at the NDR acts as a bidirectional phasing barrier. In RSC-depleted cells, this barrier has a smaller footprint, resulting in narrower NDRs. Thus, RSC plays a critical role in organizing yeast chromatin.
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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.