Characteristics of transposable element exonization within human and mouse

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.

Figure 1. Bias toward exonization at the 5′ end of the CDS.

TE-derived exons (left panels) and alternatively spliced cassette exons that did not originated from TEs (right panels) are shown in normalized locations along the CDS in increments of 0.1 (exon locations were normalized between 0 and 1, see Materials and Methods) for (A) human and (B) mouse. The x-axis is the normalized CDS location and the y-axis is the number of alternative exons.

Figure 2. Density of SNPs within all transposed elements in the human genome.

The average SNP frequency in the TE-body and the flanking sequences is shown in a sliding window of 50 bp. All frequencies are normalized to a frequency per 100 bp. The center of the TE is located at position 0.

Figure 3. Density of SNPs within all transposed elements in the mouse genome.

The average SNP frequency in the TE and the flanking sequence is shown in a sliding window of 50 bp. All frequencies are normalized to a frequency per 100 bp. The center of the TE is located at position 0.

Figure 4. Exonization of Alu element in NR_024561 dependent on RNA editing.

Editing was inferred from alignment of cDNAs to human genomic DNA. (A) Schematic illustration of exons 2 to 4 of the non-coding gene NR_024561. Exons are depicted as blue boxes. The Alu-exon, derived from AluJo (marked AEx; shown by purple box), is in an antisense orientation and is shown in the middle. The intronic, sense-orientation Alu sequence (AluS) is 731 base-pairs downstream of the exonized Alu. Sense and antisense Alus are expected to form double-stranded RNA, thus allowing RNA editing. RNA editing changes an AA dinucleotide into a functional AG 3′ splice site (lower panel). RNA editing also occurs in three positions in the Alu-derived exon (E1, E2, and E3). (B) Predicted folding of the sense and antisense Alu sequences (upper and lower lines, respectively). Adenosines that undergo editing are marked by red. Splice sites utilized for Alu exonization are marked as 5′ss and 3′ss on the alignment. (C) Alignment of this region from four species: human, gorilla, orangutan, and rhesus. The 5′ splice site, 3′ splice site, and the three editing positions are marked in yellow.