Effects of HIV Rev on Host Cell Gene Expression

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It is well established that all retroviruses have evolved processes to overcome the usual regulatory mechanisms of the cell that control or restrict the nucleocytoplasmic export of RNA until splicing is complete. A hallmark of every retroviral transcriptome is that viral mRNA with at least one retained intron reaches the cytoplasm. In the case of HIV infected cells, many different viral RNAs with one or two retained introns appear in the cytoplasm, and it is the binding of the Rev protein to a cis-acting element, the Rev Response Element (RRE), present in all of these RNAs, that facilitates this process. This proposal will explore the hypothesis that, in addition to facilitating the export and expression of viral RNAs with retained introns, Rev interacts with RNA elements present in bona fide cellular genes and human endogenous retroviruses, to overcome the mechanisms that normally control and restrict the export of RNA isoforms with retained introns. Novel RNA isoforms, whose expression has been dysregulated by Rev, may function to change the milieu of the infected cell to affect innate immunity and/or promote viral replication, either directly, or by being translated into a novel protein isoforms. The proposal has 2 specific aims: In Aim #1 we will identify cellular RNAs that functionally interact with Rev. This will be accomplished through the use of a novel vector-trap system. This will allow the isolation of cellular sequences that function like RREs (cRREs) and identify genes with potential to be regulated by Rev. In Aim #2 we will perform RNASeq on SupT1 cells transduced with retroviral vectors that express Rev or both Tat and Rev and identify genes that have novel RNA isoforms expressed in the cytoplasm. At the completion of this R21, we expect to have determined whether HIV Rev can induce the cytoplasmic expression of novel RNA species at the post-transcriptional level through interaction with cRREs. Further experiments, beyond the scope of this two year proposal, will analyze how this novel Rev-mediated post-transcriptional regulation of cellular RNAs influences HIV replication and cellular functions.