Characteristics of transposable element exonization within human and mouse

TL;DR

This study investigates how transposable elements become exonized in human and mouse genes, revealing biases, population-specific patterns, and the role of RNA editing in this process, which impacts transcriptome and proteome diversity.

Contribution

It provides new insights into the evolutionary constraints, population variability, and mechanisms like RNA editing influencing transposable element exonization in mammals.

Findings

Exonization biased towards the beginning of coding sequences.

Exonization can be population-specific, affecting divergence.

RNA editing influences primate-specific Alu element exonization.

Abstract

Insertion of transposed elements within mammalian genes is thought to be an important contributor to mammalian evolution and speciation. Insertion of transposed elements into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization. Elucidation of the evolutionary constraints that have shaped fixation of transposed elements within human and mouse protein coding genes and subsequent exonization is important for understanding of how the exonization process has affected transcriptome and proteome complexities. Here we show that exonization of transposed elements is biased towards the beginning of the coding sequence in both human and mouse genes. Analysis of single nucleotide polymorphisms (SNPs) revealed that exonization of transposed elements can be population-specific, implying that exonizations may enhance divergence and lead to speciation. SNP density analysis revealed differences between Alu and other transposed elements. Finally, we identified cases of primate-specific Alu elements that depend on RNA editing for their exonization. These results shed light on TE fixation and the exonization process within human and mouse genes.