Mammalian Transposons

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INTRODUCTION - Mammalian L1 elements (long interspersed repeated DNA elements, also called LINE-1) replicate (retrotranspose) by copying their RNA transcripts into DNA which are then integrated into the genome. The ~6 kb human L1 element has four regions: a 5 prime untranslated (UTR) regulatory region; open reading frame (ORF) 1 encodes an RNA binding protein; ORF2 encodes an endonuclease and reverse transcriptase; the 3 prime UTR contains a conserved G-rich polypurine motif. L1 elements replicate by using the 3 prime OH of the nicked target DNA to prime cDNA synthesis of its transcript. L1 can also replicate other elements (e.g., SINEs such as the Alu family) by this process. As L1 activity has persisted in mammals since their emergence and the products of L1 replication are largely retained, it is not surprising that at least 30% (860 Mb) of the working draft of the human genome (WDHG) was generated by L1 activity: 460 Mb is L1 DNA and 360 Mb is SINE DNA. In addition to their sheer mass, L1 elements, and their SINE offspring, can cause genetic rearrangements and inactivate or alter gene activity. We have used the tools of molecular biology and evolution and population genetics to examine the interaction between L1 and its host and how L1 activity might affect modern humans. RECENT FINDINGS: ANALYSIS OF AN ONGOING L1 AMPLIFICATION EVENT IN HUMANS - Our earlier studies showed that the human Ta L1 family (L1PA1), shown by others to causes in utero insertional mutations, arose ~5 Myr ago and subsequently differentiated into two major subfamilies, Ta0 and Ta1. Ta1, which had not been described earlier, is younger than Ta0 and now accounts for at least 50 % of the Ta family. As the Ta1 family only recently emerged, we reasoned that the human genome sequencing effort would miss a significant number of the Ta1 inserts in the human population. Such inserts could have medical importance as robust genetic markers both for mapping medically relevant traits and for examining the history and structure of human populations. As important, a comprehensive collection of Ta1 inserts will provide a real time view of the initial stages of an L1 amplification event, before it has been remodeled by host responses (e.g., selection) or blurred by the accumulation of elements. We devised an unbiased method to collect Ta1 inserts from four ethnic groups: African pygmy, Caucasian Druze, Chinese, Melanesian. Although most of our analysis is still ongoing, our preliminary results are striking: First, we recovered 277 of the ~300 Ta1 inserts estimated earlier. Second, as predicted, a full 40% of these inserts are not present in the current working draft of the human genome (WDHG). Third, almost 30% of the Ta1 inserts occurred in 31 discrete genomic regions (hotspots). This clustering is statistically significant and would not have been recognized by reliance on the L1 composition of the WDHG. Bioinformatic analysis of these hotspots and the loci harboring 30 non-clustered Ta1 inserts has yet to reveal an explanation for the hot spots. However, half of the 61 examined genomic loci contain genes highly expressed in testis or early embryogenesis. At this point in our analysis it is tempting to speculate that the first stage of a successful L1 amplification may involve invasion of these genomic regions. ADAPTIVE EVOLUTION IN L1 - We had earlier found that the coiled-coil motif of L1 ORF 1 had undergone episodes of adaptive evolution early in hominid evolution and that this ceased during the evolution of L1 in the African apes (human, chimpanzee, gorilla). As coiled-coil domains often mediate protein-protein interaction we reasoned that evolutionary change in this motif could reflect interaction of L1 with host factors. We have now shown that this idea has merit. A cell culture based retrotransposition assay revealed that the ancestral coiled-coil domain is active in the context of an otherwise fully modern element. Thus, the adaptive changes are not a response to changes elsewhere in the element but may reflect a response to changes in the host. We are using the cytoplasmic yeast two hybrid assay to examine such possible L1-host interactions. So far we have shown that ORF1 proteins (including those containing an ancestral coiled-coil motif) strongly self interact. The cessation of adaptive evolution in the African ape lineage suggests that the host environment for L1 may have changed dramatically after African and Asian (orangutan) apes diverged. Determining whether such a change also occurred in the Asian lineage should help illuminate the nature of the interaction between L1 and its host.