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Evaluating the protein coding potential of exonized transposable element sequences.

Jittima Piriyapongsa1, Mark T Rutledge, Sanil Patel

  • 1School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.

Biology Direct
|November 27, 2007
PubMed
Summary
This summary is machine-generated.

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Transposable elements (TEs) exonized in genomes are often assumed to encode proteins, but this study reveals they have low protein-coding potential. Many exonized TEs likely function as gene expression regulators rather than protein-coding sequences.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Transposable elements (TEs) are increasingly recognized for their functional contributions to host genomes.
  • Exonization of TEs into host mRNAs is common, but their role as protein-coding sequences is debated.
  • Investigating the actual protein-coding potential of exonized TEs is crucial for understanding genome evolution.

Purpose of the Study:

  • To evaluate ascertainment biases in detecting TE-derived protein-coding sequences (CDS).
  • To probabilistically assess the protein-coding potential of TE-derived exons.
  • To clarify the functional role of exonized TEs in host genomes.

Main Methods:

  • Comparison of sequence similarity search methods (HMM, BLAST, RepeatMasker) for TE-derived sequence detection.

Related Experiment Videos

  • Probabilistic codon-frequency analysis of TE-derived exon sequences.
  • Analysis of experimentally characterized protein datasets and genome-wide searches.

    • Main Results:

    • Profile-based methods (HMM) showed higher sensitivity and selectivity in detecting TE-derived sequences.
    • Despite sensitive methods, few additional TE-derived CDS were identified in curated datasets compared to genome-wide searches.
    • Probabilistic analysis indicated low average protein-coding potential for TE-derived exons, especially for non-autonomous TEs like Alu elements.

    Conclusions:

    • The exaptation of exonized TEs as protein-coding sequences may be less common than previously assumed.
    • Exonized TEs might primarily function as post-transcriptional regulators of gene expression via RNA pathways.
    • High copy numbers and dispersed nature suggest exonized TEs could act as master gene expression regulators.