RNA secondary and higher-order structures are known to play a fundamental role in the life cycle of RNA viruses. Several studies have indicated the existence of large-scale RNA structures in the genomes of positive-sense RNA viruses (Davis et al. J Virol 2008). Interestingly, the presence of genome-scale ordered RNA structures (GORS) corelates with host persistence, suggesting an evolutionarily conserved role for such large-scale secondary structures in the genomes of positive-sense RNA viruses.
We hypothesize that the viral genomic RNA forms multiple dynamic structures that are critical to the viral life cycle. To investigate this, we use in vitro and live cell selective 2’ hydroxyl acylation analyzed by primer extension (SHAPE) to explore the structure of viral RNAs in several biological states, including during viral translation, replication, packaging, and within viral particles. The goal of this work is to provide a comprehensive model for the dynamics and regulation of viral genomic RNA during the entire viral life cycle.
What Structure(s) Do Viral RNAs Form to Carry Out Their Business?
Open Questions
Which regions of the viral genome mediate stability, translation, replication, and packaging?
How are these events regulated?
What host and/or viral factors interact with the different regions of the genome?
How can we interrogate protein-RNA and RNA-RNA interactions on a genome-wide scale?
How can we interfere with these structures and interactions?
What can viruses teach us about cellular RNA regulation?
Significance
The characterization of novel RNA regulatory motifs will allow us to define RNA regulatory elements in viral genome(s), refine models for viral RNA replication and packaging, and aid in the design of RNA structure-based inhibitors. A broader understanding of the dynamic structure of viral RNA during various stages of the viral life cycle will allow us to uncover novel mechanisms of regulation of RNA in an effort to better understand how RNA structure modulates its biological function.
Check out some of our work on the topic:
Rheault M, Cousineau SE, Fox DR, Abram QH, and Sagan SM. Elucidating the distinct contributions of miR-122 in the HCV life cycle reveals insights into virion assembly (2023). Nucleic Acids Res. 51(5):2447-2463.
Chahal J, Gebert LFR, Camargo C, MacRae IJ, and Sagan SM*.miR-122-based Therapies Select for Three Distinct Resistance Mechanisms Based on Alterations in RNA Structure. (2021) PNAS USA. Aug 17; 118(33):e2103671118.
Chahal J, Gebert LFR, Gan HH, Camacho E, Gunsalus KC, MacRae IL, and Sagan SM. miR-122 and Ago interactions with the HCV genome alter the structure of the viral 5' terminus. (2019) Nucleic Acids Res. Apr 3. In press.
Sagan SM, Chahal J, and Sarnow P. cis-acting RNA elements in the Hepatitis C virus RNA genome. Virus Res (2015) S1068-1702(14):00543-7.
Davis M, Sagan SM, Pezacki JP, Evans DJ, and Simmonds P. Bioinformatic and Physical Characterisation of Genome-Scale Ordered RNA Structure (GORS) in Mammalian RNA Viruses. J. Virol. (2008) Sep; 82 (23):11824-11836.