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Related Concept Videos

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Gene Evolution - Fast or Slow?02:05

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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
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Targeted in Situ Mutagenesis of Histone Genes in Budding Yeast
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The impact of the nucleosome code on protein-coding sequence evolution in yeast.

Tobias Warnecke1, Nizar N Batada, Laurence D Hurst

  • 1Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.

Plos Genetics
|November 8, 2008
PubMed
Summary

DNA structure influences gene evolution. Nucleosome positioning, a DNA-level constraint, slows coding sequence evolution at synonymous and non-synonymous sites, impacting codon and amino acid choices.

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Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Genomics

Background:

  • Coding sequence evolution was traditionally attributed solely to protein function.
  • Selection also acts at the RNA level, affecting translation speed and splicing.
  • DNA structure itself may impose constraints on coding sequence evolution.

Purpose of the Study:

  • To investigate whether DNA-level constraints, specifically nucleosome positioning, influence coding sequence evolution.
  • To compare the evolutionary rates of coding sequences located in nucleosome-bound versus nucleosome-free regions.

Main Methods:

  • Utilized high-resolution microarray data in yeast.
  • Compared evolutionary rates of coding sequences associated with or free from nucleosomes.
  • Controlled for gene expression levels and intra-gene location.

Main Results:

  • Nucleosome-free (linker) sequences evolve 5-6% slower at synonymous sites compared to nucleosome-bound sequences.
  • This reduced evolutionary rate is prominent at the 5' end of genes, affecting non-synonymous rates too.
  • Codons disfavoring nucleosome formation and specific amino acid compositions are enriched in linker regions.

Conclusions:

  • DNA-level selection for nucleosome positioning impacts codon and amino acid choices.
  • Nucleosome positioning influences both synonymous and non-synonymous rates of coding sequence evolution.
  • Findings support the exclusion model of nucleosome positioning and offer new interpretations for codon usage patterns.