Reading TE leaves: new approaches to the identification of transposable element insertions

Abstract

Transposable elements (TEs) are a tremendous source of genome instability and genetic variation. Of particular interest to investigators of human biology and human evolution are retrotransposon insertions that are recent and/or polymorphic in the human population. As a consequence, the ability to assay large numbers of polymorphic TEs in a given genome is valuable. Five recent manuscripts each propose methods to scan whole human genomes to identify, map, and, in some cases, genotype polymorphic retrotransposon insertions in multiple human genomes simultaneously. These technologies promise to revolutionize our ability to analyze human genomes for TE-based variation important to studies of human variability and human disease. Furthermore, the approaches hold promise for researchers interested in nonhuman genomic variability. Herein, we explore the methods reported in the manuscripts and discuss their applications to aspects of human biology and the biology of other organisms.

Figure 1.

Recently active human retrotransposons (Long Terminal Repeat [LTR] and non-LTR groups) and their approximate representation in the human genome (in parentheses). While all sharing a polyA tail, the non-LTR retrotransposons are structurally distinct. The autonomous LINE-1 element (L1) contains two open reading frames while Alu and SVA do not. Alu is instead composed of two monomers linked by an A-rich linker sequence (A₅TACA₆). SVA is a composite element made up of a hexamer repeat of varying copy number, an Alu-like region, a region of variable numbers of tandem repeats, and an HERV-K derived region known as SINE-R. All non-LTR elements are flanked by target site duplications (arrows) that are typically between 5 and 10 bp. The only recently active LTR element in the human genome (HERV-K) has a distinct structure resembling most endogenous retroviruses—full-length copies contain a central region encoding the Gag, Pol, and Env proteins flanked by identical long terminal repeats and short TSDs. HERV-K was assayed only by Huang et al. (2010), exhibited relatively low insertion rates compared to non-LTR retrotransposons, and will not be mentioned further. L1, Alu, and SVA all mobilize via a mechanism known as TPRT (Target Primed Reverse Transcription; for review, see Ostertag and Kazazian 2001). During this process, the mobilizing element is transcribed via RNA pol II (LINE-1 and SVA) or RNA polIII (Alu). In the case of LINE-1, ORFs 1 and 2 are translated on the ribosomes and ORF1 will typically bind to its own transcript for transport back to the nucleus. Once in the nucleus, ORF1, which has endonuclease and reverse transcriptase activity, is responsible for creating and integrating a cDNA copy at some other location. Alu, and likely SVA elements, “hijack” the L1 enzymatic machinery, probably via docking to the ribosome, in order to facilitate their own nuclear reentry and reverse transcription (Boeke 1997; Ostertag et al. 2003).

Figure 2.

Schematic illustrating the mechanism of 3′ transduction by non-LTR retrotransposons and possible gene-related impacts. TE-mediated 3′ transduction occurs when the transcription machinery skips a weak or nonexistent polyadenylation signal (pA). Transcription continues until a downstream polyadenylation signal is recognized. The resulting transcript will contain a portion of the 3′ genomic flank and a secondary homopolymer tract, which will be reverse transcribed into cDNA upon reinsertion into the genome (Boeke and Pickeral 1999; Moran et al. 1999; Goodier et al. 2000). If the transduced sequence contains an exon, it may be inserted near existing exons, resulting in an exon shuffling event. Assuming RNA pol II transcription and normal post-transcriptional processing, two or more exons in the transduced sequence may be merged and reinserted, resulting in a processed pseudogene.