I elements and the Drosophila genome

Human endogenous retroviruses: from infectious elements to human genes

Mammalian genomes contain a heavy load (42% in humans) of retroelements, which are mobile sequences requiring reverse transcription for their replicative transposition. A significant proportion of these elements is of retroviral origin, with thousands of sequences resembling the integrated form of infectious retroviruses, with two LTRs bordering internal regions homologous to the gag, prt, pol, and env genes. These elements, named endogenous retroviruses (ERVs), are most probably the proviral remnants of ancestral germ-line infections by active retroviruses, which have thereafter been transmitted in a Mendelian manner. The complete sequencing of the human genome now allows a comprehensive survey of human ERVs (HERVs), which can be grouped according to sequence homologies into approximately 80 distinct families, each containing a few to several hundred elements. As reviewed here, strong similarities between HERVs and present-day retroviruses can be inferred from phylogenetic analyses on the reverse transcriptase (RT) domain of the pol gene or the transmembrane subunit (TM) of the env gene, which disclose interspersion of both classes of elements and suggest a common history and shared ancestors. Similarities are also observed at the functional levels, since despite the fact that most HERVs have accumulated mutations, deletions, and/or truncations, several elements still possess some of the functions of retroviruses, with evidence for viral-like particle formation, and occurrence of envelope proteins allowing cell-cell fusion and even conferring infectivity to pseudotypes. Along this line, a genomewide screening for human retroviral genes with coding capacity has revealed 16 fully coding envelope genes. These genes are transcribed in several healthy tissues including the placenta, three of them at a very high level. Besides their impact in modelling the genome, HERVs thus appear to contain still active genes, which most probably have been subverted by the host for its benefit and should be considered as bona fide human genes. Some of their characteristic features and possible physiological roles, as well as potential pathological effects inherited from their retroviral ancestors are also reviewed.

Survey of human genes of retroviral origin: identification and transcriptome of the genes with coding capacity for complete envelope proteins

Sequences of retroviral origin occupy approximately 8% of the human genome. Most of these "retroviral" genes have lost their coding capacities since their entry into our ancestral genome millions of years ago, but some reading frames have remained open, suggesting positive selection. The complete sequencing of the human genome allowed a systematic search for retroviral envelope genes containing an open reading frame and resulted in the identification of 16 genes that we have characterized. We further showed, by quantitative reverse transcriptase PCR using specifically devised primers which discriminate between coding and noncoding elements, that all 16 genes are expressed in at least some healthy human tissues, albeit at highly different levels. All envelope genes disclose significant expression in the testis, three of them have a very high level of expression in the placenta, and a fourth is expressed in the thyroid. Besides their primary role as key molecules for viral entry, the envelope genes of retroviruses can induce cell-cell fusion, elicit immunosuppressive effects, and even protect against infection, and as such, endogenous retroviral envelope proteins have been tentatively identified in several reports as being involved in both normal and pathological processes. The present study provides a comprehensive survey of candidate genes and tools for a precise evaluation of their involvement in these processes.

UVB irradiation upregulation of the Drosophila 1731 retrotransposon LTR requires the same short sequence of U3 region in a human epithelial cell line as in Drosophila cells

Phylogenetic analysis of the retrotransposon and retrovirus suggests an evolutionary relationship between them and indicates that transactivation of the long terminal repeat (LTR)-containing retroelements could be ubiquitous. Using constructs expressing a reporter gene under the control of the entire or deleted LTR of 1731, which is a retrotransposable element of Drosophila melanogaster, we were able to show that the UVB-irradiation activation of the 1731-LTR requires the same short sequence of U3 region in a human epithelial cell line as in Schneider's Drosophila cell line (S2). This sequence is similar to the binding sequence of the members of the nuclear factor-kappa B (NF-kappa B)/rel family. In addition, human colonic carcinoma cells (HT29), in response to UVB-irradiation, produce some extracellular factor(s) that activates the 1731-LTR in nonirradiated cells.

Defective I elements introduced into Drosophila as transgenes can regulate reactivity and prevent I-R hybrid dysgenesis

The I-R hybrid dysgenesis syndrome is characterized by a high level of sterility and I element transposition, occurring in the female offspring of crosses between males of inducer (I) strains, which contain full-length transposable I elements, and females of reactive (R) strains, devoid of functional I elements. The intensity of the syndrome in the dysgenic cross is essentially dependent on the reactivity level of the R females, which is ultimately controlled by still unresolved polygenic chromosomal determinants. In the work reported here, we have introduced a transposition-defective I element with a 2.6 kb deletion within its second open reading frame into a highly reactive R strain, by P-mediated transgenesis. We demonstrate that this defective I element gradually alters the level of reactivity in the three independent transgenic lines that were obtained, over several generations. After > 15 generations, the transgenic Drosophila show strongly reduced reactivity, and finally become refractory to hybrid dysgenesis, without, however, acquiring the inducer phenotype. Induction of a low reactivity level is reversible--reactivity again increases upon transgene removal--and is maternally inherited, as observed for the control of reactivity in natural R strains. These results demonstrate that defective I elements introduced as single-copy transgenes can act as regulators of reactivity, and suggest that some of the ancestral defective pericentromeric I elements that can be found in all reactive strains could be the molecular determinants of reactivity.