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Doublet preference and gene evolution.

R Hanai1, A Wada

  • 1Department of Physics, Faculty of Science, University of Tokyo, Japan.

Journal of Molecular Evolution
|February 1, 1990
PubMed
Summary
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DNA doublet preferences in bacteria and yeast mirror noncoding regions, suggesting mutational biases shaped both coding and noncoding DNA sequences over evolutionary time.

Area of Science:

  • Genomics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • DNA sequences exhibit non-random patterns in nucleotide dinucleotide frequencies (doublets).
  • These doublet preferences can vary between coding and noncoding regions within genomes.
  • Understanding these patterns offers insights into evolutionary pressures and mutational processes.

Purpose of the Study:

  • To analyze doublet preferences in coding and noncoding DNA across different organisms (E. coli, S. cerevisiae, human).
  • To investigate correlations between doublet preferences in coding and noncoding regions.
  • To propose a mechanism explaining observed doublet preference correlations.

Main Methods:

  • Comparative analysis of DNA sequences from Escherichia coli, Saccharomyces cerevisiae, and human (mitochondrial and nuclear).

Related Experiment Videos

  • Examination of doublet frequencies (1-2, 2-3, 3-1) in both coding and noncoding genomic regions.
  • Correlation analysis between doublet preferences in different sequence contexts.

    • Main Results:

    • Doublet preference patterns in coding regions of E. coli and S. cerevisiae correlated with their noncoding regions.
    • A similar correlation was observed for the 3-1 doublet in specific E. coli and S. cerevisiae gene sets.
    • Evidence suggests mutational biases influenced noncoding doublet preferences, which subsequently affected coding regions.

    Conclusions:

    • Mutational biases likely established doublet preferences in noncoding DNA.
    • These biases subsequently influenced doublet preferences in coding DNA, particularly where coding constraints were relaxed.
    • The findings provide a unified mechanism for doublet preference evolution across coding and noncoding DNA.