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The gene-orientation structure of eukaryotes.

Gordon Simons1, Glenn Morton

  • 1Department of Statistics, College of Arts and Sciences, The University of North Carolina at Chapel Hill, CB 3260, 301 New West 3260 Cameron Avenue, Chapel Hill, NC 27599-3260, USA. simons@stat.unc.edu

Journal of Theoretical Biology
|June 5, 2003
PubMed
Summary

Gene orientations in four eukaryotes are modeled by Markov chains. Parameters suggest organism-wide regulation, not just chromosome-specific, ruling out random gene shuffling.

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Area of Science:

  • Genomics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Gene order and orientation are fundamental genomic features.
  • Understanding patterns in gene orientation across eukaryotes can reveal evolutionary and regulatory mechanisms.

Purpose of the Study:

  • To model the sequence of gene orientations in four diverse eukaryotes.
  • To investigate whether Markov chain parameters are chromosome-dependent or organism-dependent.

Main Methods:

  • Application of a two-state, two-parameter first-order Markov chain model.
  • Analysis of gene orientation sequences from nematodes (C. elegans), yeast (S. cerevisiae), Arabidopsis (A. thaliana), and fruit flies (D. melanogaster).
  • Statistical scrutiny of model parameters to determine dependency.

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Main Results:

  • Gene orientation sequences in the studied eukaryotes are well-modeled by Markov chains.
  • A simpler, one-parameter symmetric Markov chain also provides a reasonable model.
  • Statistical evidence strongly suggests that Markov chain parameters are organism-dependent, not chromosome-dependent.

Conclusions:

  • The observed organism-dependent gene orientation parameters require biological explanation, possibly involving inter-chromosomal communication or common environmental origins.
  • A simple random shuffling of genes via mutations does not explain the observed patterns.