ArticlePLoS genetics2013
A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription.
Article in PLoS genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed, 145 citations in OpenAlex.
- Context-dependent interplay of Swi-Snf and Tup1-Cyc8 influences chromatin and transcription at antagonistically regulated genes.Nature communications · 2026Article
- Nucleosome positioning shapes cryptic antisense transcription.PLoS genetics · 2026Article
- Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation.Genome research · 2026Article
- The histone chaperone Spt6 controls chromatin structure through its conserved N-terminal domain.Molecular cell · 2025Article
- The histone chaperone Spn1 preserves chromatin protections at promoters and nucleosome positioning in open reading frames.G3 (Bethesda, Md.) · 2025Article
- Overlapping and distinct functions of SPT6, PNUTS, and PCF11 in regulating transcription termination.Nucleic acids research · 2025Article
- The yeast genome is globally accessible in living cells.Nature structural & molecular biology · 2025Article
- Article
- Energy-driven genome regulation by ATP-dependent chromatin remodellers.Nature reviews. Molecular cell biology · 2024Review
- Size fractionated NET-Seq reveals a conserved architecture of transcription units around yeast genes.Yeast (Chichester, England) · 2024Article
- A single fiber view of the nucleosome organization in eukaryotic chromatin.Nucleic acids research · 2024Article
- Insights into Spt6: a histone chaperone that functions in transcription, DNA replication, and genome stability.Trends in genetics : TIG · 2023Review
- Nucleosome retention by histone chaperones and remodelers occludes pervasive DNA-protein binding.Nucleic acids research · 2023Article
- The conserved histone chaperone Spt6 is strongly required for DNA replication and genome stability.Cell reports · 2023Article
- A role for the Saccharomyces cerevisiae Rtt109 histone acetyltransferase in R-loop homeostasis and associated genome instability.Genetics · 2022Article
- Partitioned usage of chromatin remodelers by nucleosome-displacing factors.Cell reports · 2022Article
- Distinct functions of three chromatin remodelers in activator binding and preinitiation complex assembly.PLoS genetics · 2022Article
- Pitfalls in using phenanthroline to study the causal relationship between promoter nucleosome acetylation and transcription.Nature communications · 2022Article
- SWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genes.Nature communications · 2022Article
- The biogenesis and function of nucleosome arrays.Nature communications · 2021Article
27 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain to be identified. We profiled a compendium of 50 yeast strains carrying conditional alleles or complete deletions of genes involved in transcriptional regulation, histone biology, and chromatin remodeling, as well as compounds that target transcription and histone deacetylases, to assess their respective roles in nucleosome positioning and transcription. We find that nucleosome patterning in genes is affected by many factors, including the CAF-1 complex, Spt10, and Spt21, in addition to previously reported remodeler ATPases and histone chaperones. Disruption of these factors or reductions in histone levels led genic nucleosomes to assume positions more consistent with their intrinsic sequence preferences, with pronounced and specific shifts of the +1 nucleosome relative to the transcription start site. These shifts of +1 nucleosomes appear to have functional consequences, as several affected genes in Ino80 mutants exhibited altered expression responses. Our parallel expression profiling compendium revealed extensive transcription changes in intergenic and antisense regions, most of which occur in regions with altered nucleosome occupancy and positioning. We show that the nucleosome-excluding transcription factors Reb1, Abf1, Tbf1, and Rsc3 suppress cryptic transcripts at their target promoters, while a combined analysis of nucleosome and expression profiles identified 36 novel transcripts that are normally repressed by Tup1/Cyc8. Our data confirm and extend the roles of chromatin remodelers and chaperones as major determinants of genic nucleosome positioning, and these data provide a valuable resource for future studies.
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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.