Thanks to movies like Jurassic Park, DNA and RNA molecules may be best known as coding sequences used to build a living creature. For some viruses, however, these nucleic acids are more than just pages of instructions; they’re also critical tools that enable them to infiltrate and hijack a host cell, forcing it to produce more viral particles.
Since emerging in 2019, the SARS-CoV-2 virus—perhaps the most infamous RNA virus today—has evolved into several different variants, each carrying mutations that set them apart from the original strain. Researchers such as A*STAR Genome Institute of Singapore (A*STAR GIS) Senior Scientist Siwy Ling Yang are keen to learn just how these mutations alter the shapes of viral RNA, thereby boosting (or reducing) a strain’s ability to survive and reproduce.
“Like proteins, RNAs can fold into complex shapes to perform various functions. These shapes are particularly important in RNA viruses, as they use RNA to interact with both their own genomes and with host RNA,” said Yang.
In a recent investigation into links between genome structure and function across SARS-CoV-2 variants, Yang worked alongside Yue Wan, a Principal Investigator at A*STAR GIS; Roland Huber, Principal Scientist at the A*STAR Bioinformatics Institute (A*STAR BII); and Andres Merits of the University of Tartu, Estonia. The team included colleagues from A*STAR GIS; A*STAR Infectious Diseases Labs (A*STAR IDL); A*STAR Institute of Molecular and Cell Biology (A*STAR IMCB); Duke-NUS Medical School, Singapore; and the University of California in the US.
The researchers focused on a key component of RNA shape: a connection known as long-range RNA-RNA pairing. “Imagine such a pairing as a long piece of string with Velcro patches placed near both ends, which then make contact and stick together,” said Wan. “The resulting carefully folded shapes allow viruses to control protein production, genome copying and packaging using molecular structure, rather than extra genes.”
Using high-throughput structure-probing techniques to process multiple samples simultaneously, the team modelled and compared the genomes of wild-type SARS-CoV-2 with the Alpha, Beta, Delta and Omicron variants to identify shared structures linked to viral fitness.
SHAPE-MaP modelling revealed that across all strains, SARS-CoV-2 RNA structures could fold into many complex shapes, with structures generally unchanged between variants. However, even single-nucleotide variations or interactions with RNA-binding proteins could impact RNA shapes in all strains.
“Interestingly, we also discovered that a shared ultra-long-range RNA-RNA interacting structure, LR1, binds directly to a host protein called ADAR1,” said Huber. “This binding appears to facilitate edits on the viral genome that enable more successful proliferation.”
The team also found that disrupting LR1 decreased virus replication in host cells, and that LR1 seemed to bind to SARS-CoV-2’s protein shell, hinting at a potential role in packaging the viral genome.
These results highlight the functional impact of RNA structures in SARS-CoV-2 and may help direct treatment research. “Understanding the RNA architecture of SARS-CoV-2 provides critical insights into how the virus maintains infectivity despite mutations,” said Yang. “These discoveries could inform the development of next-generation therapeutics aimed at destabilising viral RNA structures, rather than targeting proteins alone.”
The A*STAR-affiliated researchers contributing to this research are from the A*STAR Genome Institute of Singapore (A*STAR GIS), A*STAR Bioinformatics Institute (A*STAR BII), A*STAR Infectious Diseases Labs (A*STAR IDL) and A*STAR Institute of Molecular and Cell Biology (A*STAR IMCB).
