RNAi siRNA-induced DNA methylation of HIV-1 LTR

Investigating the central role of integration in HIV-1 –Mpho Mosia
Human immunodeficiency virus (HIV) is a global pandemic that requires alternative
therapeutic strategies, especially due to its latency which presents a major hurdle to
virus eradication in infected individuals. Although the current standard of treatment,
HAART seems to have had a significant improvement in prognosis, challenges related
to high costs, toxicity, patient compliance, and resistance associated with the life-long
treatment regimen, remain to be obstacles for adequate disease maintenance.
Previous studies have almost invariably focussed on exploring integration if HIV-1 viral
genomes, as an essential step of the retrovirus life-cycle. However, this integrated viral
DNA represents only a minor part of reverse-transcribed genomes.
What was once considered to be “dead-end” episomal DNA that renders nonintegrated
HIV-1 forms replication-defective, is now being deemed to be a myth. Nonintegrated
HIV-1 genomes have recently been reported to play a role in contributing
to viral propagation, persistence and treatment escape, thus demonstrating their
capability to aid in the regulation of HIV-1 latency.
This notion is supported by a number of studies revealing the help of integrated proviral
DNA in packaging episomally transcribed viral genomes into infectious particles, which
may contribute to their capability of expressing important HIV-1 regulatory proteins
such as those encoded by nef and tat.
Interestingly, the countenance of episomal HIV-1 is associated with epigenetic
silencing. In vitro studies have demonstrated increased expression of non-integrated
HIV-1 from exposure to histone deacetylase inhibitors (HDACi), a feature associated
transcriptionally silenced chromatin.
Furthermore, demethylating agents within the 5’ Long-terminal repeat (LTR) region of
HIV-1 provirus in chronically infected cell lines leads to the notion that perhaps
epigenetic is a preceding silencing is a mechanism which leads to subsequent nonintegrated
HIV-1 transcription and the expression of nef and tat proteins.
In this current era of gene-based therapeutics, RNA interference (RNAi) is increasingly
becoming a renowned field in the quest for conquering infectious disease. Small
interfering RNA (siRNA), one of the major contributing research tools in this field,
shows promise as an antiviral mechanism, which could better our understanding in
transcriptional processes for identifying drug targets to better manage HIV-1 latency.
Recently, studies reveal HIV-1 specific siRNAs to possess potent antiviral effects in a
variety of cell culture systems containing cognate sequences existing within different
regions of the HIV-1 genome. This subsequently culminates to inhibition of HIV
infection by specifically degrading genomic HIV-1 RNA in a number of systems
including permanent cell lines, primary CD4 positive T cells and macrophages.
Moreover, promoter methylation, shown to prolong the suppressive effect of siRNA on
productive HIV-1 infection, has been reported to result in transient suppression of the
virus through the degradation of viral transcripts. In this regard, CpG methylation of
important episomal genes of non-integrated HIV-1 DNA expressing nef and tat

proteins seems to be a promising knock-down approach that could lead to the
eradicating HIV-1 latency.
In this respect, I aim to investigate non-integrated HIV-1 genomes by siRNA-induced
promoter methylation, specifically in the 5’ LTR of this burdensome retroviral disease.