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Related Experiment Videos

Universal rule for coding sequence construction: TA/CG deficiency-TG/CT excess.

S Ohno1

  • 1Beckman Research Institute of the City of Hope, Durate, CA 91010.

Proceedings of the National Academy of Sciences of the United States of America
|December 1, 1988
PubMed
Summary
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Coding sequences show a universal rule: frequent CT and TG dimers are balanced by rare CG and TA dimers. This base composition pattern, observed across diverse species, impacts gene regulation.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • DNA base composition is finite, leading to interdependencies between oligomer frequencies.
  • Previous studies identified CTG as a frequent trimer in coding sequences, with underrepresented CG and TA dimers.

Purpose of the Study:

  • To investigate the universality of base dimer underrepresentation in coding sequences.
  • To analyze coding sequences from diverse species (human, plant, fish) with varying base compositions.

Main Methods:

  • Analysis of three new and one previously studied coding sequences.
  • Examination of base dimer frequencies (CT, TG, CG, TA) within these sequences.

Main Results:

  • The excess of CT and TG dimers, and complementary deficiency of CG and TA dimers, was a consistent finding.

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  • This pattern held true even in sequences with lopsided base compositions not favoring CT or TG.

    • Conclusions:

    • A universal rule for coding sequence construction is proposed, characterized by excess CT/TG and deficient CG/TA dimers.
    • The underrepresentation of CG and TA dimers in coding sequences may explain the dual nature of regulatory signals in intergenic regions.