Retroviral genomic RNA dimer partner selection
Jessica Anne Flynn, University of Michigan, United States
University of Michigan . Awarded
Retroviruses such as human immunodeficiency virus (HIV-1) and Moloney murine leukemia virus (MLV) package dimers of their RNA genome, a conformation which is beneficial for genetic recombination. Although genomic RNAs are generally identical and thus recombinants are indistinguishable from either parent, two distinct RNAs can be copackaged when virions are produced by coinfected cells. Within the cytoplasm of these cells, it has been assumed that RNA dimer partner selection is random, yielding encapsidated RNA homo- and heterodimers in Hardy-Weinberg proportions, a presumption critical for calculating retroviral recombination rates.
In this thesis, MLV and HIV-1 RNA homo- and heterodimerization were examined using native Northern blotting as well as a novel RNA dimer capture assay. The results demonstrated that while HIV-1 RNAs formed homo- and heterodimers in random proportions, MLV RNAs preferentially self-associated. The resultant MLV virion population contained less than 40% of the heterodimers expected from random dimerization and indicated that MLV recombination rates have previously been underestimated. Coexpressed MLV vector RNAs which differed from each other in sequence by less than 0.1% self-associated to the same extent as RNAs that were similar only in their packaging regions, suggesting that homology sensing is not the mechanism of biased RNA homodimerization.
Additionally, we explored the hypothesis that the distance between proviral templates might affect MLV heterodimer formation. To do this, genetically distinct MLV RNA transcripts were produced either from two cotransfected vectors or from a single genetic locus, and the proportions of hetero- and homo dimeric virion RNAs were monitored and compared. Unlike RNAs generated from two different templates, the RNAs transcribed from a single template dimerized at random. These findings suggest a model in which MLV RNA dimer partner selection occurs either cotranscriptionally or within a pool of transcripts near the proviral template.
Flynn, J.A. Retroviral genomic RNA dimer partner selection. Ph.D. thesis, University of Michigan. Retrieved February 23, 2019 from https://www.learntechlib.org/p/117402/.
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