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Centripetal modules and ancient introns.

S W Roy1, M Nosaka, S J de Souza

  • 1Harvard University, The Biological Laboratories, Cambridge, MA 02138, USA.

Gene
|November 26, 1999
PubMed
Summary
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We developed an algorithm to identify protein modules, finding that ancient intron positions correlate with these structural boundaries, supporting a mixed theory of intron evolution.

Area of Science:

  • Computational Biology
  • Molecular Evolution
  • Bioinformatics

Background:

  • Introns are non-coding DNA sequences in eukaryotes.
  • The origin and evolution of introns remain debated.
  • Protein structure modules offer a potential framework for understanding intron-exon relationships.

Purpose of the Study:

  • To investigate the relationship between protein structural modules and intron positions.
  • To test the hypothesis that ancient introns are associated with protein structural boundaries.
  • To explore the evolutionary history of introns using computational methods.

Main Methods:

  • Developed an algorithm to define protein modules based on centripetal definition.
  • Analyzed 44 ancient conserved proteins with known structures and intron positions.

Related Experiment Videos

  • Correlated intron positions (phase zero, one, and two) with identified module boundaries.
  • Examined phylogenetic distribution of introns to identify putatively ancient intron positions.

    • Main Results:

    • Phase zero intron positions significantly correlate with 'centripetal' module boundaries (p = 0.0002).
    • Phase one and two intron positions do not show significant correlation with module boundaries.
    • A subset of 120 putatively 'ancient' introns are significantly closer to module boundaries than the full set of phase zero introns (p = 0.008).

    Conclusions:

    • The findings support a mixed theory of intron evolution.
    • Some introns are ancient and were involved in early exon shuffling.
    • Intron gain and loss have occurred throughout evolutionary history.