Transposable Elements: Insertion Pattern and Impact on Gene Expression Evolution in Hominids

Abstract

Transposable elements (TEs) can affect the regulation of nearby genes through several mechanisms. Here, we examine to what extent recent TE insertions have contributed to the evolution of gene expression in hominids. We compare expression levels of human and chimpanzee orthologs and detect a weak increase in expression divergence (ED) for genes with species-specific TE insertions compared with unaffected genes. However, we show that genes with TE insertions predating the human-chimpanzee split also exhibit a similar increase in ED and therefore conclude that the increase is not due to the transcriptional influence of the TEs. These results are further confirmed by lineage-specific analysis of ED, using rhesus macaque as an outgroup: Human-chimpanzee ortholog pairs, where one ortholog has suffered TE insertion but not the other, do not show increased ED along the lineage where the insertion occurred, relative to the other lineage. We also show that genes with recent TE insertions tend to produce more alternative transcripts but find no evidence that the TEs themselves promote transcript diversity. Finally, we observe that TEs are enriched upstream relative to downstream of genes and show that this is due to insertional bias, rather than selection, because this bias is only observed in genes expressed in the germ line. This provides an alternative neutral explanation for the accumulation of TEs in upstream sequences.

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

“…In animals, genome-wide studies have produced evidence that TEs contribute to divergence in gene expression between rodent species (37) but not between primates (38). Surprisingly, the relationship between TE proximity and gene expression level varies between A. lyrata and A. thaliana; in all of our analyses, gene expression in A. thaliana appeared more sensitive to the proximity of TEs.…”

Characterization and functional annotation of nested transposable elements in eukaryotic genomes

“…Nested TE genes can participate in gene regulation, with potential to increase the diversity and complexity of gene regulation and promote expression divergence [13]. In mammals, interspersed repeats are over-represented and evolutionarily associated with defense response genes [24].…”

“…Depending on the site of insertion this can result in the creation of novel genes [9], new nested genes [10,11], or different types of TEs [12]. DNA transposons are preferentially associated with the euchromatic, or genic, component of genomes and show an insertion bias in the upstream sequences of genes [13]. This can immediately affect gene regulation and function and may have significant biological and evolutionary consequences in eukaryotic genomes [14].…”

Mechanisms of Transposable Element Evolution in Plants and Their Effects on Gene Expression

“…TE insertional polymorphisms have been noted to favor high single-nucleotide polymorphism (SNP) regions in rice, supporting the former hypothesis [105]. Likewise in humans and chimpanzees, TEs were found to insert close to genes with more diverged expression levels due to TE insertion site preference rather than any effect of the TEs on proximal genes [106].…”