The Long and Short of Virus Genomes

Short- and long-range interactions that give structure to virus genomes also influence virus replication and infectiousness.


Deceptively simple in their biological makeup, viruses typically consist of genetic material enclosed in a protein coat. In the case of dengue and Zika viruses, a single long strand of RNA encodes everything the virus needs to replicate inside a host. Like a string, the RNA molecule can fold onto itself, forming structures in which certain genomic sequences come close to each other in physical space, with implications for virus infectivity and reproduction.

In the present study, researchers led by Yue Wan at A*STAR’s Genome Institute of Singapore (GIS) mapped in detail the genome structures of the four serotypes of dengue viruses and four geographically distinct Zika viruses. The first challenge they had to overcome was the very large size of the genomes, each about 11,000 bases long, which makes structural modeling of the genomes very inaccurate.

To get around this problem, Wan’s team combined two methods—Selective 2′ Hydroxyl Acylation analyzed by Primer Extension (SHAPE) and mutational mapping (MaP)—to first identify single-stranded bases in the genome. This was followed by another technique known as Sequencing of Psoralen-crosslinked, Ligated, and Selected Hybrids (SPLASH), which reveals pairs of genomic regions that are linked in physical space.

The combination of short-range structure information from SHAPE-MaP and long-range structure information from SPLASH allowed the researchers to build accurate structural models of the virus genomes. Using their models, they uncovered two distinct modes of long-range interactions in the virus genomes. The first interaction type preserves the exact spatial locations as well as the sequences of the interaction across serotypes, while the second type involves different sequences in nearby spatial locations that bring two distant regions of the genome into close proximity.

“Disrupting these long-range RNA interactions can result in a large decrease in virus fitness, as fewer virus particles were produced in infected cells,” Wan explained, noting that similar results were observed in virus-infected animal models.

“The genomes of dengue and Zika viruses also interact with host RNAs inside infected cells. We are now studying how virus-host RNA interactions affect virus fitness. We are also working with collaborators to study genome organization in other RNA viruses, including the chikungunya virus and enteroviruses,” she said.

The A*STAR-affiliated researchers contributing to this research are from the Genome Institute of Singapore (GIS) and Bioinformatics Institute (BII).