Characterization of a natural heterodimer between MLV genomic RNA and the SD′ retroelement generated by alternative splicing

Murine leukemia virus (MLV) specifically packages both genomic RNA (FL RNA) and a subgenomic RNA, which we call SD′. SD′ RNA results from alternative splicing of FL RNA. It is reverse-transcribed, and its DNA copy, integrated into the host genome, constitutes a splice donor-associated retroelement. FL and SD′ RNAs share a common 5′-UTR that includes the packaging/dimerization signal (Psi). To investigate whether the mechanism of copackaging of these two RNAs involves RNA heterodimerization, we examined the spontaneous dimerization capacity of the two RNAs as large synthetic RNAs transcribed in vitro. We showed that SD′ RNA not only formed homodimers with similar efficiency as the FL RNA, but that FL and SD′ RNAs also formed FL/SD′ heterodimers via Psi sequences. Comparison of the thermostabilities determined for these different dimeric species and competition experiments with Psi RNA fragments indicate the recruitment of similar dimer-linkage interactions within the Psi region. To validate these results, the dimeric state of the SD′ RNA was analyzed in MLV particles. RNA capture assays performed with the FL RNA as bait revealed that SD′, and not the host packageable U6 or 7SL RNAs, was associated with the FL RNA in virions. Heterodimerization of SD′ RNA with FL RNA may argue for the recent concept of a nuclear dimerization at or near the site of transcription and raises the new hypothesis of RNA dimerization during splicing. Furthermore, FL/SD′ heterodimerization may have leukemogenic consequences by influencing the pool of genomic dimers that will undergo recombinogenic template switching by reverse transcriptase. Published by Cold Spring Harbor Laboratory Press.