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Related Concept Videos

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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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In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
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Variation in synonymous codon use and DNA polymorphism within the Drosophila genome.

N Bierne1, A Eyre-Walker

  • 1Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton, UK. n-bierne@univ-montp2.fr

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Selective constraints on protein evolution, not genetic draft, explain codon usage bias variation in Drosophila. Protein evolution is a stable factor, while local interference is unstable over evolutionary time.

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Area of Science:

  • Evolutionary biology
  • Genomics
  • Molecular evolution

Background:

  • A negative correlation exists between amino acid substitution rates and codon usage bias in Drosophila.
  • This correlation is hypothesized to result from interference between positive selection on protein sequences and weak selection on codon usage.

Purpose of the Study:

  • To investigate polymorphism and divergence at synonymous, nonsynonymous, and intronic sites in relation to codon bias.
  • To determine the relative contributions of protein evolution and local interference (genetic draft) to codon bias variation.

Main Methods:

  • Analysis of polymorphism and divergence data in Drosophila melanogaster and Drosophila simulans.
  • Comparison of variation patterns across synonymous, nonsynonymous, and intronic sites.
  • Assessment of correlation between genetic variation, recombination rates, and codon usage bias.

Main Results:

  • Protein evolution significantly explains codon bias variation (r² ≈ 40%).
  • Synonymous and intronic diversities did not significantly covary with codon bias or protein evolution.
  • Polymorphism levels decreased in low recombination regions, but codon bias did not.
  • Nonsynonymous diversities were correlated across species, but synonymous and intronic diversities were not.

Conclusions:

  • Selective constraint on proteins is a stable factor in gene evolution, whereas local interference (genetic draft) is unstable.
  • Genetic draft appears to be a minor determinant of codon bias variance.
  • Selective constraints for optimal codon usage are likely correlated with selective constraints on the protein, both within and between genes.