Regulation of Endogenous Retroviruses and Cellular Genes by HIV-1 Rev

Retroviruses infect humans as well as many species of vertebrate animals and are the causative agent of diseases, to include immune deficiencies, malignancies and neurological disorders. These single-stranded RNA viruses, are reverse transcribed into cDNA and are irreversibly integrated into the human genome. The most well studied exogenous retrovirus, infects the somatic cells of the host, is human immunodeficiency virus (HIV-1). Retroviruses found within our genome, endogenous retroviruses (ERVs), were once exogenous, but have since infected the germline and are transmitted to their offspring. Approximately 8% of the human genome is comprised of several, almost complete ERV proviral copies, and numerous fragments.
During HIV-1 infection, it has been reported that there are significant changes in host cell gene expression to include changes of host cell mRNA isoforms with retained introns and induction of gene expression of human endogenous retroviruses (HERVs). The mechanisms underlying this differential host gene expression during HIV-1 infection are not well understood. However, it is known that two of the HIV-1 regulatory proteins, Rev and Tat, are essential for viral replication. Tat promotes HIV transcription, while Rev serves to promote the nucleo-cytoplasmic export and expression of unspliced or incompletely spliced viral mRNAs by binding to the cis-acting Rev Response Element (RRE). This is similar to the role played by the HERV-K Rec protein, which binds to the HERV-K Rec Response Element (RcRE) in HERV-K mRNAs. Since Rev has been shown to function with a prototypical RcRE, it is proposed that during HIV-1 infection, Rev may play a similar role to HERV-K Rec. The functional interaction between Rev and RcREs or similar structures, would result in changes in cellular gene expression through export and expression of novel mRNA isoforms, including HERV-K derived mRNAs.
A combination of bioinformatics, RNAseq, and cell-based functional assays were used to study the changes in host cell gene expression. Potential RcREs were identified through a number of bioinformatic approaches, then tested for their ability to promote export and translation of a reporter mRNA with a retained intron in conjunction with Rev or Rec. Some of the selected elements functioned well with either Rev, Rec or both, whereas some showed little or no function. Rev function on individual RcREs varied and was also dependent on the Rev sequence. To investigate host gene expression, RNAseq analysis was performed on total and cytoplasmic RNA isolated from T-lymphocyte cells transduced with HIV Rev, Tat, Rev and Tat, or HERV-K Rec. Proviral mRNA from three HERV-K loci, 4p16.1b, 22q11.23 and most significantly 3q12.3, accumulated in the presence of Rev or Tat and Rev, but not Rec. One HERV-K LTR5A, 592, was significantly expressed in the cytoplasm, in the presence of Tat and Rev, and is consistently transcribed during HIV infection in different cell types. The results from this study indicate that in addition to HERV transcription, transcripts with retained introns are increased in cytoplasmic RNA when Tat and Rev are expressed together. The results from RNAseq gene and transcript expression analysis revealed that HIV-1 Rev is capable of regulating cholesterol biosynthesis, which has been previously attributed to only HIV-1 Nef. Taken together, these results suggest that HIV Rev or Rev and Tat together, are capable of modulating gene and mRNA isoform expression, during HIV-1 infection.