Emerging Opportunities to Study Mobile Element Insertions and Their Source Elements in an Expanding Universe of Sequenced Human Genomes

Abstract

Three mobile element classes, namely Alu, LINE-1 (L1), and SVA elements, remain actively mobile in human genomes and continue to produce new mobile element insertions (MEIs). Historically, MEIs have been discovered and studied using several methods, including: (1) Southern blots, (2) PCR (including PCR display), and (3) the detection of MEI copies from young subfamilies. We are now entering a new phase of MEI discovery where these methods are being replaced by whole genome sequencing and bioinformatics analysis to discover novel MEIs. We expect that the universe of sequenced human genomes will continue to expand rapidly over the next several years, both with short-read and long-read technologies. These resources will provide unprecedented opportunities to discover MEIs and study their impact on human traits and diseases. They also will allow the MEI community to discover and study the source elements that produce these new MEIs, which will facilitate our ability to study source element regulation in various tissue contexts and disease states. This, in turn, will allow us to better understand MEI mutagenesis in humans and the impact of this mutagenesis on human biology.

Keywords: Alu; L1; LINE-1; SVA; human genomes; mobile element insertions.

Figure 1

L1 retrotransposition cycle. The L1 retrotransposition cycle that produces a new L1 insertion (MEI) is depicted. Full-length L1 source elements with two intact ORFs encode potentially active ORF1p and ORF2p proteins (upper left—ORF1 in light green, ORF2 in dark green). In this case, the L1 source element is located on chromosome 17 (Chr17). The source element is transcribed from the internal L1 promoter (arrow) to generate L1 mRNA (blue). The L1 mRNA is exported to the cytoplasm, where the ORF1 and ORF2 regions are translated to produce ORF1p and ORF2p. These proteins bind to the mRNA that generated them through a process called cis-preference to generate an L1 RNP. The RNP is imported back into the nucleus, where the process of target-primed reverse transcription (TPRT) uses the mRNA template to generate an L1 MEI at a new genomic location. In this case, the new insertion is located on chromosome 5 (Chr5). A double-stranded L1 MEI likely is generated by similar steps as the first strand. Note that new insertions frequently are 5′ truncated (as depicted) and are flanked by new target site duplications (red). Alu and SVA use a similar process by substituting their RNAs and hijacking the L1 machinery.