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Transposable elements and gene expression during the evolution of amniotes.

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Molecular Biology

Background:

  • Transposable elements (TEs) significantly alter genome sequences through insertions and deletions.
  • TEs can be exapted as regulatory elements, influencing gene expression patterns.
  • Tissue-specific gene expression is conserved across amniote species, suggesting conserved regulatory mechanisms.

Purpose of the Study:

  • To investigate the association between species-specific transposable element insertions and gene expression.
  • To understand the impact of TE age and type on gene expression evolution in amniotes.

Main Methods:

  • Employed a novel bootstrapping approach to analyze gene expression data from six tissues across six amniote genomes.
  • Compared gene expression of orthologs and non-orthologs with recent versus older TE insertions.

Main Results:

  • Significant differences in gene expression were associated with TE insertions in both orthologs and non-orthologs.
  • TEs were linked to species-specific gene expression changes, with notable magnitude and direction.
  • Species-specific TEs generally correlated with lower gene expression in orthologs, while non-species-specific TEs correlated with higher expression in non-orthologs, with exceptions like SINEs in humans and chickens.

Conclusions:

  • Observed species-specific TE associations with gene expression support their role in speciation and adaptation.
  • The impact of TEs on gene expression is not consistent and depends on TE age and type.
  • Extrapolating TE-gene expression associations across distantly related species should be done cautiously.