Cytosine methylation by DNMT2 facilitates stability and survival of HIV-1 RNA in the host cell during infection

Abstract

The enigmatic methyltransferase, DNMT2 (DNA methyltransferase 2), structurally resembles a DNA methyltransferase, but has been shown to be a tRNA methyltransferase targeting cytosine within a specific CpG in different tRNA molecules. We had previously shown that, during environmental stress conditions, DNMT2 is re-localized from the nucleus to the cytoplasmic stress granules (SGs) and is associated with RNA-processing proteins. In the present study, we show that DNMT2 binds and methylates various mRNA species in a sequence-independent manner and gets re-localized to SGs in a phosphorylation-dependent manner. Importantly, our results indicate that HIV-1 enhances its survivability in the host cell by utilizing this RNA methylation capability of DNMT2 to increase the stability of its own genome. Upon infection, DNMT2 re-localizes from the nucleus to the SGs and methylates HIV-1 RNA. This DNMT2-dependent methylation provided post-transcriptional stability to the HIV-1 RNA. Furthermore, DNMT2 overexpression increased the HIV-1 viral titre. This would suggest that HIV hijacks the RNA-processing machinery within the SGs to ensure its own survival in the host cell. Thus, our findings provide for a novel mechanism by which virus tries to modulate the host cell machinery to its own advantage.

Reduced levels of methyltransferase DNMT2 sensitize human fibroblasts to oxidative stress and DNA damage that is accompanied by changes in proliferation-related miRNA expression

“…Moreover, in mosquitoes ( Aedes aegypti ), the introduced endosymbiont, Wolbachia , suppressed expression of AaDnmt2 , but dengue virus (DENV) induced expression of AaDnmt2 and the authors concluded that AaDnmt2 plays an important role not only in the maintenance of Wolbachia infection in mosquito cells, but also in the resistance of mosquito cells to DENV infection [32] . Finally, it has been reported that cytosine methylation by DNMT2 promoted stability and survival of HIV-1 RNA in the host cell during infection [33] . As siRNA treatment resulted in elevated levels of beta-interferon in WI-38 and BJ cells (this study) and prolonged beta-interferon stimulation induced ROS-mediated DNA damage signaling and p53-dependent senescence in IMR90 human fibroblasts [34] , we decided then to analyze the effects of DNMT2 silencing on cell proliferation and longevity, intracellular redox equilibrium, genetic stability and epigenetic parameters.…”

“…In general, siRNA treatment, both control siRNA and DNMT2 siRNA, promoted an increase in the levels of beta-interferon in WI-38 and BJ cells (this study). More recently, the role of DNMT2 homologs during viral infections has been proposed in different biological model systems [31] , [32] , [33] . In Drosophila melanogaster , dDnmt2 has been reported to be required for innate immune responses and dDnmt2 mutant flies accumulated increasing levels of Drosophila C virus (DCV) and showed activated innate immune responses [31] .…”

Characterizing the transcriptional expression and in situ localization of the Dnmt2 gene in Drosophila willistoni

“…On the other hand, the HIV virus is able to increase its survival in the host cell using the RNA methylation activity of Dnmt2, increasing the stability of its own genome. Through infection, Dnmt2 relocates from the nucleus to the cytoplasmic stress granules and methylates the RNA virus, promoting the post-transcriptional stability of viral RNA [45]. RNAs interference (RNAi) have a strong association with different epigenetic mechanisms, such as histone methylation/acetylation and genomic DNA methylation [46].…”

Host Methyltransferases and Demethylases: Potential New Epigenetic Targets for HIV Cure Strategies and Beyond

“…So far, only DNMT1, DNMT2, and DNMT3B have been implicated in HIV infection. 31,32 DNMT1, which is the most abundant DNMT in the cell and transcribed mostly during the S phase of the cell cycle, is primarily responsible for maintaining methylation through transfer of methyl groups to the hemimethylated DNA strands after DNA replication, but also has de novo DNMT activity. 33 In addition, DNMT1 influences transcriptional regulation by interacting with HDAC2 and novel corepressors to form a complex at replication foci.…”

“…35 Recently, DNMT2 was shown to relocalize from the nucleus to stress granules and to methylate HIV-1 RNA in a sequence-independent manner, thereby providing posttranscriptional stability to the HIV-1 RNA. 32 DNMT3B, which is highly expressed in early embryonic stem (ES) cells, cannot differentiate between unmethylated and hemimethylated CpG sites, and cannot copy or contribute to the maintenance of a specific pattern of methylation. 33 However, DNMT3B has an important role in de novo methylation of unmodified cytosine residues.…”