Transposable elements: insertion pattern and impact on gene expression evolution in hominids.

Area of Science:

• Genomics
• Evolutionary Biology
• Molecular Biology

Background:

• Transposable elements (TEs) are mobile DNA sequences with the potential to influence gene regulation and evolution.
• Understanding the impact of recent TE insertions on gene expression divergence is crucial for evolutionary genomics.

Purpose of the Study:

• To investigate the contribution of recent transposable element insertions to the evolution of gene expression in hominids.
• To determine if TEs influence gene expression divergence or transcript diversity.

Main Methods:

• Comparative analysis of gene expression levels between human and chimpanzee orthologs.
• Assessment of expression divergence (ED) in genes with and without species-specific or ancient TE insertions.
• Lineage-specific analysis of ED using rhesus macaque as an outgroup.
• Examination of alternative transcript production in genes with recent TE insertions.

Main Results:

• A weak increase in expression divergence (ED) was observed for genes with species-specific TE insertions, but also for genes with ancient TE insertions, suggesting TEs are not the primary cause.
• Lineage-specific analysis confirmed that TE insertions do not correlate with increased ED along the insertion lineage.
• Genes with recent TE insertions showed a tendency for more alternative transcripts, but TEs did not directly promote this diversity.
• TEs are enriched upstream of genes, attributed to insertional bias in germline-expressed genes rather than selection.

Conclusions:

• Recent transposable element insertions have a limited role in driving gene expression evolution in hominids.
• The observed association between TEs and gene expression divergence is likely a consequence of insertional bias, particularly in germline-expressed genes.
• TEs do not appear to be a major driver of transcript diversity evolution.