In exploring methylation in HIV, researchers uncover a key to its replication

Kelsey Kaustinen
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SAN DIEGO—While therapies for treating and managing HIV have come a long way, there are still aspects of the disease left unexplored, and the investigation of one of those—methylation—has led to the discovery of a new facet of HIV’s mechanism of infection. Details of this study by researchers at the University of California, San Diego (UC San Diego), were published in a paper titled “Dynamics of the human and viral m6A RNA methylomes during HIV-1 infection of T cells,” which appeared in Nature Microbiology.
RNA is the genetic material responsible for carrying instructions from the DNA in the nucleus out to the cytoplasm of a cell, where those instructions are used to build proteins. While DNA is the main genetic material in human cells, the entire HIV genome consists of RNA, and as such, the virus can take control of its host’s cellular machinery to translate its RNA into proteins.
RNA can be chemically modified by cells in order to control or change its functions, and while one such modification, known as N6-methyladenosine (m6A), is common in humans and other organisms, not much was known about its role in the immune system. This study revealed m6A modifications in HIV RNA for the first time, and the team also looked at m6A’s impact on function in both HIV and human host RNA when human immune cells are infected.
“We and other colleagues at pharmaceutical companies have worked over the years to develop drugs targeting HIV’s genetic material, its RNA, but we never made it to the clinic,” said Dr. Tariq Rana, a professor of pediatrics at UC San Diego School of Medicine and senior author of the study. “Now we know why: We were developing drugs using RNA targets that didn’t have these modifications, when in reality the RNA was different.”
According to Gianluigi Lichinchi, a graduate student in Rana’s lab and first author of the study, “M6A had always been considered a steady modification of cellular RNA. Instead, it turned out to be extremely dynamic and highly responsive to external stimuli, such as viral infections. In the future, these findings could aid in improving the design and efficacy of HIV/AIDS vaccines.”
“[m6A] regulates RNA stability, processing, splicing and translation,” says Rana, adding that “I expect many additional mechanisms will be revealed in future.”
One protein encoded by HIV’s RNA genome is Rev. After these proteins are generated in the host cell’s cytoplasm, they migrate back into the nucleus where they assemble at a specific point on HIV RNA known as the Rev responsive element (RRE). Once there, Rev aids in transporting newly produced HIV RNA transcripts into the host cytoplasm, a critical step in the virus’ replication.
In further investigating m6A, the researchers found that m6A modification of both human and viral RNA influences the interaction between the HIV Rev protein and RRE. Specifically, when the enzyme that removes m6A from RNA is silenced, HIV replication increases; when the enzyme that adds m6A to RNA is silenced, HIV replication decreases. The team notes that this is a result that can be targeted pharmacologically to combat HIV infection.
The abstract notes that “viral infection triggers a massive increase in m6A in both host and viral mRNAs. In HIV-1 mRNA, we identified 14 methylation peaks in coding and noncoding regions, splicing junctions and splicing regulatory sequences. We also identified a set of 56 human gene transcripts that were uniquely methylated in HIV-1-infected T cells and were enriched for functions in viral gene expression. The functional relevance of m6A for viral replication was demonstrated by silencing of the m6A writer or the eraser enzymes, which decreased or increased HIV-1 replication, respectively. Furthermore, methylation of two conserved adenosines in the stem loop II region of HIV-1 Rev response element (RRE) RNA enhanced binding of HIV-1 Rev protein to the RRE in vivo and influenced nuclear export of RNA. Our results identify a new mechanism for the control of HIV-1 replication and its interaction with the host immune system.”
Rana says that the impact of methylation, specifically “epitranscriptomic modifications,” has never before been studied in HIV biology.
“The HIV field has missed this modification in physiological RNA structure and HIV genome for more than 30 years,” Rana remarked. “I will not be surprised if other viruses with RNA genomes also exploit this m6A modification mechanism to evade immune surveillance and control their replication in human cells. These viruses include, for example, influenza, hepatitis C, Ebola and Zika, just to name a few.”
He adds the team will next be investigating the mechanisms of other sites in the genome and what roles they might play in the regulation of viral-host biology and immune evasion.

Kelsey Kaustinen

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