Large-scale analysis of exonized mammalian-wide interspersed repeats in primate genomes

Abstract

Transposable elements (TEs) are major sources of new exons in higher eukaryotes. Almost half of the human genome is derived from TEs, and many types of TEs have the potential to exonize. In this work, we conducted a large-scale analysis of human exons derived from mammalian-wide interspersed repeats (MIRs), a class of old TEs which was active prior to the radiation of placental mammals. Using exon array data of 328 MIR-derived exons and RT-PCR analysis of 39 exons in 10 tissues, we identified 15 constitutively spliced MIR exons, and 15 MIR exons with tissue-specific shift in splicing patterns. Analysis of RNAs from multiple species suggests that the splicing events of many strongly included MIR exons have been established before the divergence of primates and rodents, while a small percentage result from recent exonization during primate evolution. Interestingly, exon array data suggest substantially higher splicing activities of MIR exons when compared with exons derived from Alu elements, a class of primate-specific retrotransposons. This appears to be a universal difference between exons derived from young and old TEs, as it is also observed when comparing Alu exons to exons derived from LINE1 and LINE2, two other groups of old TEs. Together, this study significantly expands current knowledge about exonization of TEs. Our data imply that with sufficient evolutionary time, numerous new exons could evolve beyond the evolutionary intermediate state and contribute functional novelties to modern mammalian genomes.

Figure 1.

Splicing signals of constitutive exons, MIR-derived exons and Alu-derived exons. (A) 5′ splice site score. (B) 3′ splice site score. (C) Density of exonic splicing enhancers (ESEs). Error bars indicate 95% confidence interval.

Figure 2.

The percentage of ‘correlated exons’ among exons derived from young transposable elements (Alu) and old transposable elements (MIR, LINE1, LINE2).

Figure 3.

Examples of ‘correlated’ mammalian-wide interspersed repeat (MIR) exons from exon array analysis, semi-quantitative RT–PCR and sequencing. In each gel figure, solid arrows show sequencing confirmed MIR exon inclusion forms. Hollow arrows show sequencing confirmed MIR exon skipping forms. Dashed arrows show sequencing confirmed non-specific PCR products.

Figure 4.

Splicing patterns of MIR exons in fibroblast cell lines of humans, chimpanzees, rhesus macaques, marmosets and mouse kidney. In each gel figure, exon inclusion forms and exon skipping forms are denoted as asterisks and arrow heads, respectively.