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Insertion of transposed elements within mammalian genes is thought to be animportant contributor to mammalian evolution and speciation. Insertion oftransposed elements into introns can lead to their activation as alternativelyspliced cassette exons, an event called exonization. Elucidation of theevolutionary constraints that have shaped fixation of transposed elementswithin human and mouse protein coding genes and subsequent exonization isimportant for understanding of how the exonization process has affectedtranscriptome and proteome complexities. Here we show that exonization oftransposed elements is biased towards the beginning of the coding sequence inboth 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. SNPdensity analysis revealed differences between Alu and other transposedelements. Finally, we identified cases of primate-specific Alu elements thatdepend on RNA editing for their exonization. These results shed light on TEfixation and the exonization process within human and mouse genes.

Characteristics of transposable element exonization within human and mouse