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Related Experiment Videos

Computational identification of putative programmed translational frameshift sites.

Atul A Shah1, Michael C Giddings, Jasmin B Parvaz

  • 1Department of Human Genetics, University of Utah, SLC, 84112-5330, USA.

Bioinformatics (Oxford, England)
|August 15, 2002
PubMed
Summary

Statistical analysis reveals underrepresented nucleotide sequences in yeast genes are linked to programmed frameshifting. This finding suggests a mechanism for producing alternative protein products, impacting gene expression.

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Area of Science:

  • Computational Biology
  • Genetics
  • Molecular Biology

Background:

  • Investigates the hypothesis that programmed frameshift sites are underrepresented in protein-coding sequences due to selective pressure.
  • Focuses on identifying and analyzing nucleotide subsequences within the Saccharomyces cerevisiae (yeast) genome.

Purpose of the Study:

  • To develop and apply a computational method for identifying underrepresented nucleotide sequences potentially involved in programmed frameshifting.
  • To evaluate the distribution of 7-base oligonucleotides (heptanucleotides) in yeast protein-coding sequences.

Main Methods:

  • Developed a computer program to compare observed nucleotide subsequence frequencies against those predicted by a zero-order Markov chain model.
  • The model was based on codon bias within the analyzed sequences.

Related Experiment Videos

  • Analyzed over 6000 putative protein-coding sequences from S. cerevisiae.

    • Main Results:

    • Identified specific heptanucleotides, including CUU-AGG-C and CUU-AGU-U, as significantly underrepresented in yeast coding sequences.
    • These underrepresented heptanucleotides are associated with programmed +1 translational frameshifts essential for producing specific yeast proteins (ABP140 and EST3).
    • Laboratory experiments confirmed that other identified underrepresented heptanucleotides, such as GGU-CAG-A, also promote significant translational frameshifting.

    Conclusions:

    • Underrepresentation of specific nucleotide sequences in yeast genes correlates with programmed translational frameshifting.
    • This suggests a potential mechanism for generating diverse protein products from a single gene.
    • The findings imply that other underrepresented heptamers may also encode transframe products, broadening the understanding of gene expression regulation.