ArticlePLoS genetics2008
The impact of the nucleosome code on protein-coding sequence evolution in yeast.
Article in PLoS genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed, 98 citations in OpenAlex.
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- Unusual mammalian usage of TGA stop codons reveals that sequence conservation need not imply purifying selection.PLoS biology · 2022Article
- Epigenetics and genome stability.Mammalian genome : official journal of the International Mammalian Genome Society · 2020Review
- EvoChromo: towards a synthesis of chromatin biology and evolution.Development (Cambridge, England) · 2019Review
- An intron-derived motif strongly increases gene expression from transcribed sequences through a splicing independent mechanism in Arabidopsis thaliana.Scientific reports · 2019Article
- NucMap: a database of genome-wide nucleosome positioning map across species.Nucleic acids research · 2019Article
- Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates.Biophysical journal · 2018Article
- Refining the Ambush Hypothesis: Evidence That GC- and AT-Rich Bacteria Employ Different Frameshift Defence Strategies.Genome biology and evolution · 2018Article
- Adenine Enrichment at the Fourth CDS Residue in Bacterial Genes Is Consistent with Error Proofing for +1 Frameshifts.Molecular biology and evolution · 2017Article
- Nucleosomal organization and DNA base composition patterns.Nucleus (Austin, Tex.) · 2017Review
- Estimating the prevalence of functional exonic splice regulatory information.Human genetics · 2017Review
- GC Content Heterogeneity Transition of Conserved Noncoding Sequences Occurred at the Emergence of Vertebrates.Genome biology and evolution · 2016Article
- Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome.Genome research · 2016Article
- Evidence of selection for an accessible nucleosomal array in human.BMC genomics · 2016Article
- A deformation energy-based model for predicting nucleosome dyads and occupancy.Scientific reports · 2016Article
- Genomic approaches to DNA repair and mutagenesis.DNA repair · 2015Review
- The effects of chromatin organization on variation in mutation rates in the genome.Nature reviews. Genetics · 2015Review
- Limitations of the 'ambush hypothesis' at the single-gene scale: what codon biases are to blame?Molecular genetics and genomics : MGG · 2015Article
- A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins.Open biology · 2015Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Coding sequence evolution was once thought to be the result of selection on optimal protein function alone. Selection can, however, also act at the RNA level, for example, to facilitate rapid translation or ensure correct splicing. Here, we ask whether the way DNA works also imposes constraints on coding sequence evolution. We identify nucleosome positioning as a likely candidate to set up such a DNA-level selective regime and use high-resolution microarray data in yeast to compare the evolution of coding sequence bound to or free from nucleosomes. Controlling for gene expression and intra-gene location, we find a nucleosome-free "linker" sequence to evolve on average 5-6% slower at synonymous sites. A reduced rate of evolution in linker is especially evident at the 5' end of genes, where the effect extends to non-synonymous substitution rates. This is consistent with regular nucleosome architecture in this region being important in the context of gene expression control. As predicted, codons likely to generate a sequence unfavourable to nucleosome formation are enriched in linker sequence. Amino acid content is likewise skewed as a function of nucleosome occupancy. We conclude that selection operating on DNA to maintain correct positioning of nucleosomes impacts codon choice, amino acid choice, and synonymous and non-synonymous rates of evolution in coding sequence. The results support the exclusion model for nucleosome positioning and provide an alternative interpretation for runs of rare codons. As the intimate association of histones and DNA is a universal characteristic of genic sequence in eukaryotes, selection on coding sequence composition imposed by nucleosome positioning should be phylogenetically widespread.
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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.