ArticleMolecular and cellular biology2011
Evolution of nucleosome occupancy: conservation of global properties and divergence of gene-specific patterns.
Article in Molecular and cellular biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 33 citations in OpenAlex.
- Prediction of G4 formation in live cells with epigenetic data: a deep learning approach.NAR genomics and bioinformatics · 2023Article
- A strong structural correlation between short inverted repeat sequences and the polyadenylation signal in yeast and nucleosome exclusion by these inverted repeats.Current genetics · 2019Article
- DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells.Cell research · 2017Article
- Genome-wide mapping of nucleosome positions in Saccharomyces cerevisiae in response to different nitrogen conditions.Scientific reports · 2016Article
- Evidence of selection for an accessible nucleosomal array in human.BMC genomics · 2016Article
- Nucleosome positioning in yeasts: methods, maps, and mechanisms.Chromosoma · 2015Review
- A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins.Open biology · 2015Article
- Chromatin mediation of a transcriptional memory effect in yeast.G3 (Bethesda, Md.) · 2015Article
- Clustered regulatory elements at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe.BMC genomics · 2013Article
- Conserved substitution patterns around nucleosome footprints in eukaryotes and Archaea derive from frequent nucleosome repositioning through evolution.PLoS computational biology · 2013Article
- Noise-mean relationship in mutated promoters.Genome research · 2012Article
- Comparative studies of gene expression and the evolution of gene regulation.Nature reviews. Genetics · 2012Review
- Nucleosome organization affects the sensitivity of gene expression to promoter mutations.Molecular cell · 2012Article
- Nucleosome positioning: bringing order to the eukaryotic genome.Trends in cell biology · 2012Review
- Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping.Open biology · 2012Article
- Nucleosome Positioning.ISRN molecular biology · 2012Review
- Comparative analyses of homocitrate synthase genes of ascomycetous yeasts.International journal of evolutionary biology · 2012Article
- Abundant gene-by-environment interactions in gene expression reaction norms to copper within Saccharomyces cerevisiae.Genome biology and evolution · 2012Article
- Promoter nucleosome organization shapes the evolution of gene expression.PLoS genetics · 2012Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 4 countries.
Funding
Abstract
To examine the role of nucleosome occupancy in the evolution of gene expression, we measured the genome-wide nucleosome profiles of four yeast species, three belonging to the Saccharomyces sensu stricto lineage and the more distantly related Candida glabrata. Nucleosomes and associated promoter elements at C. glabrata genes are typically shifted upstream by ∼20 bp, compared to their orthologs from sensu stricto species. Nonetheless, all species display the same global organization features first described for Saccharomyces cerevisiae: a stereotypical nucleosome organization along genes and a division of promoters into those that contain or lack a pronounced nucleosome-depleted region (NDR), with the latter displaying a more dynamic pattern of gene expression. Despite this global similarity, however, nucleosome occupancy at specific genes diverged extensively between sensu stricto and C. glabrata orthologs (∼50 million years). Orthologs with dynamic expression patterns tend to maintain their lack of NDR, but apart from that, sensu stricto and C. glabrata orthologs are nearly as similar in nucleosome occupancy patterns as nonorthologous genes. This extensive divergence in nucleosome occupancy contrasts with a conserved pattern of gene expression. Thus, while some evolutionary changes in nucleosome occupancy contribute to gene expression divergence, nucleosome occupancy often diverges extensively with apparently little impact on gene expression.
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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.