Carnivore-specific SINEs (Can-SINEs): distribution, evolution, and genomic impact

Abstract

Short interspersed nuclear elements (SINEs) are a type of class 1 transposable element (retrotransposon) with features that allow investigators to resolve evolutionary relationships between populations and species while providing insight into genome composition and function. Characterization of a Carnivora-specific SINE family, Can-SINEs, has, has aided comparative genomic studies by providing rare genomic changes, and neutral sequence variants often needed to resolve difficult evolutionary questions. In addition, Can-SINEs constitute a significant source of functional diversity with Carnivora. Publication of the whole-genome sequence of domestic dog, domestic cat, and giant panda serves as a valuable resource in comparative genomic inferences gleaned from Can-SINEs. In anticipation of forthcoming studies bolstered by new genomic data, this review describes the discovery and characterization of Can-SINE motifs as well as describes composition, distribution, and effect on genome function. As the contribution of noncoding sequences to genomic diversity becomes more apparent, SINEs and other transposable elements will play an increasingly large role in mammalian comparative genomics.

Figure 1

Alignment and minimum evolution phylogeny of Repbase Can-SINE voucher sequences. All Can-SINE vouchers begin with the designation “SINEC,” followed by species of first discovery where “Fc” = Felis catus, “CF” = Canis familiaris, “Ame” = Ailuropoda melanoleuca, and “Pv” = Phoca vitulina. (A) The initial global alignment of lysine-tRNA derived segments was estimated using the Geneious alignment module (Drummond et al. 2010) and refined by hand. Lines indicate RNA polymerase III promoter boxes A and B. (B) The neighbor-joining clustering algorithm was used to estimate phylogeny with the Tamura–Nei distance model, and branch support approximated using 1000 bootstrap replications. Feliform SINEs form a distinct clade.

Figure 2

Retrotransposition of mammalian SINE insertions. (A) The master SINE copy is transcribed by RNA polymerase III. (B) LINE-derived enzyme nicks a chromosome strand at the motif AATTTT. (C) The poly-A tail of a transcribed SINE binds to the free TTTT and acts as a primer for LINE-derived reverse transcriptase. A nick on the opposite strand frees the complementary target site duplication sequence. (D) Reverse transcriptase synthesizes complementary strands. (E) A new SINE insertion with characteristic target site duplications. Adapted from (Cordaux and Batzer 2009). (This figure appears in color in the online version of Journal of Heredity.)