期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2015
卷号：112
期号：12
页码：3692-3697
DOI：10.1073/pnas.1416266112
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：SignificancePlus-sense RNA viruses cause diverse pathologies in humans. Viral RNA genomes are selected to encode information both in their primary sequences and in their higher-order tertiary structures required to replicate and to evade host immune responses. We interrogated the physical structures of three evolutionarily divergent hepatitis C virus (HCV) RNA genomes using high-throughput chemical probing and found, along with all previously known RNA-structure-based regulatory elements, diverse previously uncharacterized structures that impact viral replication. We also characterized strategies by which the HCV genomic RNA structure masks detection by innate immune sensors. This structure-first strategy for comparative analysis of genome-wide RNA structure can be broadly applied to understand the contributions of higher-order genome structure to viral replication and pathogenicity. Hepatitis C virus (HCV) infects over 170 million people worldwide and is a leading cause of liver disease and cancer. The virus has a 9,650-nt, single-stranded, messenger-sense RNA genome that is infectious as an independent entity. The RNA genome has evolved in response to complex selection pressures, including the need to maintain structures that facilitate replication and to avoid clearance by cell-intrinsic immune processes. Here we used high-throughput, single-nucleotide resolution information to generate and functionally test data-driven structural models for three diverse HCV RNA genomes. We identified, de novo, multiple regions of conserved RNA structure, including all previously characterized cis-acting regulatory elements and also multiple novel structures required for optimal viral fitness. Well-defined RNA structures in the central regions of HCV genomes appear to facilitate persistent infection by masking the genome from RNase L and double-stranded RNA-induced innate immune sensors. This work shows how structure-first comparative analysis of entire genomes of a pathogenic RNA virus enables comprehensive and concise identification of regulatory elements and emphasizes the extensive interrelationships among RNA genome structure, viral biology, and innate immune responses.
