Newly Identified Families of Human Endogenous Retroviruses

Abstract

Human endogenous retroviruses (HERVs) make up approximately 8.3% of the human genome (12). HERVs have previously been classified into 31 distinct families based upon sequence alignment of reverse transcriptase (RT) and envelope domains and subsequent phylogenetic analyses (1, 9, 16). Using the data mining program LTR_STRUC (13) in conjunction with conventional sequence homology techniques, we recently completed an analysis of chimpanzee long terminal repeat (LTR) retrotransposon families (unpublished data). Since LTR_STRUC searches for LTR retrotransposons based on structure (e.g., the presence of LTRs, target site duplications, tRNA binding sites, etc.) rather than homology, elements can be identified that go undetected in traditional BLAST searches. We identified nine chimpanzee LTR retrotransposon families that are orthologous to HERV families not previously identified. These nine newly discovered HERV families are described and characterized in this letter. LTR retrotransposons and retroviruses are grouped into three major classes (14). Class I contains elements related to gammaretroviruses, class II elements are related to betaretroviruses, and class III elements are related to spumaviruses. The RT-based phylogeny indicates that all the newly identified HERVs described here are class I elements (Fig. ​(Fig.1).1). The detailed characteristics of each of the newly discovered HERV families are presented in Table ​Table11 and Table ​Table2.2. All are low-abundance families, being composed of only one to seven full-length members with low homology to previously identified HERVs. This may, in part, explain why they have not been previously identified. The newly discovered full-length elements are of standard HERV length (7,198 to 10,675 bp with 359- to 682-bp LTRs) and display typically sized target site duplications (4 or 5 bp). With the exception of a few mutated copies, the newly identified elements have the same canonical dinucleotides terminating the LTRs as previously characterized HERVs (TG/CA). Since LTR_STRUC can only identify elements having two LTRs, we conducted BLAST searches by using identified full-length elements as query sequences to identify solo LTRs and other fragmented elements. Consistent with what has been reported previously for other HERV families (15), we have found that each of the newly identified families is represented by significantly more solo LTRs and fragmented sequences than full-length elements (Table ​(Table11). FIG. 1. Unrooted RT-based neighbor-joining tree of human LTR retrotransposon families. The phylogenetic tree is built from the DNA sequence (using MEGA3 software [11]) of the RTs taken from all the members of the newly identified HERV families together with representative ... TABLE 1. Representative elements of human LTR retrotransposon families characterized in this study TABLE 2. Characteristics of human LTR retrotransposon families identified in this study Because HERV LTRs are synthesized from the same RNA template during reverse transcription, they are identical in sequence at the time of integration (2). Using a primate pseudogene nucleotide substitution rate of 0.16% divergence/million years (5, 8, 10), the relative integration time or age of any full-length HERV can be estimated from the level of sequence divergence existing between the element's 5′ and 3′ LTRs. Using this method, the estimated ages of the new families of HERVs described here range from 18.0 to 49.5 million years, indicating that members of these families have not been transpositionally active in the primate lineage since well before chimpanzees and humans diverged from a common ancestor (6 million years ago) (4). Although caution must be taken when using LTR divergence to estimate the ages of individual elements because of confounding processes such as recombination and conversion (e.g., see references 6 and 7), the method is able to provide useful age estimates, at least to a first approximation (e.g., see reference 3). Our estimated ages of the newly identified human elements fall within the median range of previously described families of HERVs (16). The possible contribution of these newly identified LTR retrotransposons to primate gene or genome evolution is currently under investigation.