ArticlePLoS biology2010
The role of nucleosome positioning in the evolution of gene regulation.
Article in PLoS biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 142 papers.
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Who cites it
142 citing papers in PubMed, 230 citations in OpenAlex.
- Emergence Biases in Molecular Evolution.Genome biology and evolution · 2026Review
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- Sequence and chemical specificity define the functional landscape of intrinsically disordered regions.Nature cell biology · 2026Article
- Nanoscale Characterization of Interaction of Nucleosomes with H1 Linker Histone.International journal of molecular sciences · 2024Article
- Balanced Training Sets Improve Deep Learning-Based Prediction of CRISPR sgRNA Activity.ACS synthetic biology · 2024Article
- In silico design of DNA sequences for in vivo nucleosome positioning.Nucleic acids research · 2024Article
- Comprehensive Identification and Characterization of HML-9 Group in Chimpanzee Genome.Viruses · 2024Article
- SWI/SNF complex-mediated chromatin remodeling iniScience · 2024Article
- Species-aware DNA language models capture regulatory elements and their evolution.Genome biology · 2024Article
- Energy-driven genome regulation by ATP-dependent chromatin remodellers.Nature reviews. Molecular cell biology · 2024Review
- Natural trait variation across Saccharomycotina species.FEMS yeast research · 2024Review
- Parallel Nonfunctionalization of CK1δ/ε Kinase Ohnologs Following a Whole-Genome Duplication Event.Molecular biology and evolution · 2023Article
- Parallel nonfunctionalization of CK1δ/ε kinase ohnologs following a whole-genome duplication event.bioRxiv : the preprint server for biology · 2023Article
- Comparing Mitochondrial Activity, Oxidative Stress Tolerance, and Longevity of ThirteenAntioxidants (Basel, Switzerland) · 2023Article
- Article
- Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.G3 (Bethesda, Md.) · 2023Article
- Evolution of transcription factor binding through sequence variations and turnover of binding sites.Genome research · 2022Article
- GC content strongly influences the role of poly(dA) in the intrinsic nucleosome positioning in Saccharomyces cerevisiae.Yeast (Chichester, England) · 2022Article
- Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica.Nature communications · 2022Article
- Identification of Taxonomically Restricted Transcripts from Illumina RNA Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2022Article
82 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
5 authors at 3 institutions in 1 country.
Funding
Abstract
Chromatin organization plays a major role in gene regulation and can affect the function and evolution of new transcriptional programs. However, it can be difficult to decipher the basis of changes in chromatin organization and their functional effect on gene expression. Here, we present a large-scale comparative genomic analysis of the relationship between chromatin organization and gene expression, by measuring mRNA abundance and nucleosome positions genome-wide in 12 Hemiascomycota yeast species. We found substantial conservation of global and functional chromatin organization in all species, including prominent nucleosome-free regions (NFRs) at gene promoters, and distinct chromatin architecture in growth and stress genes. Chromatin organization has also substantially diverged in both global quantitative features, such as spacing between adjacent nucleosomes, and in functional groups of genes. Expression levels, intrinsic anti-nucleosomal sequences, and trans-acting chromatin modifiers all play important, complementary, and evolvable roles in determining NFRs. We identify five mechanisms that couple chromatin organization to evolution of gene regulation and have contributed to the evolution of respiro-fermentation and other key systems, including (1) compensatory evolution of alternative modifiers associated with conserved chromatin organization, (2) a gradual transition from constitutive to trans-regulated NFRs, (3) a loss of intrinsic anti-nucleosomal sequences accompanying changes in chromatin organization and gene expression, (4) re-positioning of motifs from NFRs to nucleosome-occluded regions, and (5) the expanded use of NFRs by paralogous activator-repressor pairs. Our study sheds light on the molecular basis of chromatin organization, and on the role of chromatin organization in the evolution of gene regulation.
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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.