Alu elements are the most successful transposons in humans. They are 300-bp non-coding sequences transcribed by RNA polymerase III (Pol III) and are expected to retrotranspose with the aid of reverse transcriptases of cellular origin. We previously showed that human LINEs can generate cDNA copies of any mRNA transcript by means of a retroposition process involving reverse transcription and integration by the LINE-encoded endonuclease and reverse transcriptase. Here we show mobility of marked Alu sequences in human HeLa cells with the canonical features of a retrotransposition process, including splicing out of an autocatalytic intron introduced into the marked sequence, target site duplications of varying lengths and integrations into consensus A-rich sequences. We further show that the poly-A stretch at the Alu 3' end is essential for mobility, that LINEs are required for transposition and that the rate of retroposition is 100-1,000 times higher for Alu transcripts than for control mRNAs, thus accounting for the high mutational activity of these elements observed in humans.

Endogenous retroviruses are multicopy retroelements accounting for nearly 10% of murine or human genomes. These retroelements spread into our ancestral genome millions of years ago and have acted as a driving force for genome evolution. Endogenous retroviruses may also be deleterious for their host, and have been implicated in cancers and autoimmune diseases. Most retroelements have lost replication competence because of the accumulation of inactivating mutations, but several, including some murine intracisternal A-particle (IAP) and MusD sequences, are still mobile. These elements encode a reverse transcriptase activity and move by retrotransposition, an intracellular copy-and-paste process involving an RNA intermediate. The host has developed mechanisms to silence their expression, mainly cosuppression and gene methylation. Here we identify another level of antiviral control, mediated by APOBEC3G, a member of the cytidine deaminase family that was previously shown to block HIV replication. We show that APOBEC3G markedly inhibits retrotransposition of IAP and MusD elements, and induces G-to-A hypermutations in their DNA copies. APOBEC3G, by editing viral genetic material, provides an ancestral wide cellular defence against endogenous and exogenous invaders.

Human Endogenous Retroviruses are expected to be the remnants of ancestral infections of primates by active retroviruses that have thereafter been transmitted in a Mendelian fashion. Here, we derived in silico the sequence of the putative ancestral "progenitor" element of one of the most recently amplified family-the HERV-K family-and constructed it. This element, Phoenix, produces viral particles that disclose all of the structural and functional properties of a bona-fide retrovirus, can infect mammalian, including human, cells, and integrate with the exact signature of the presently found endogenous HERV-K progeny. We also show that this element amplifies via an extracellular pathway involving reinfection, at variance with the non-LTR-retrotransposons (LINEs, SINEs) or LTR-retrotransposons, thus recapitulating ex vivo the molecular events responsible for its dissemination in the host genomes. We also show that in vitro recombinations among present-day human HERV-K (also known as ERVK) loci can similarly generate functional HERV-K elements, indicating that human cells still have the potential to produce infectious retroviruses.[Supplemental material is available online at www.genome.org.]Nearly 8% of the human genome is composed of sequences of retroviral origin. Most of them are degenerate, either due to recombination between the two provirus LTRs or to mutations interrupting the retroviral ORFs. The env gene seems to be best conserved, with 18 intact genes retaining a full coding capacity in the human genome (Benit et al. 2001;de Parseval et al. 2003;Villesen et al. 2004), possibly because of its potential role in human physiology. The HERV-K(HML2) family of endogenous retroviruses is an exception to this general rule, since some copies still contain complete ORFs for the other retroviral genes (Löwer et al. 1996; for review, see Bannert and Kurth 2004). This family includes the most recently amplified endogenous retroviruses, most of which have integrated into the genome <5 million years ago, with a few insertions showing polymorphism within the human population (Steinhuber et al. 1995;Medstrand and Mager 1998;Barbulescu et al. 1999;Turner et al. 2001;Hughes and Coffin 2004;Belshaw et al. 2005). Some of these recently integrated proviruses are responsible for the synthesis of retroviral particles that can be observed in teratocarcinoma and melanoma-derived cell lines Löwer et al. 1993;Bieda et al. 2001;Muster et al. 2003;Buscher et al. 2005), and possibly in human placenta (Kalter et al. 1973;Dirksen and Levy 1977;Wilkinson et al. 1994). Because of this "activity," the HERV-K(HML2) family has been the subject of numerous studies in the past years, with the description of alleles with nearly intact proviruses and complete coding capacity (Mayer et al. 1999;Reus et al. 2001;Turner et al. 2001). Despite these efforts, no functional provirus able to produce infectious particles has yet been described. Even if several loci containing complete ORFs have been identified, and in spite of the availability of the comp...