Biophysical Society Thematic Meeting| Santa Cruz 2018

Genome Biophysics: Integrating Genomics and Biophysics to Understand Structural and Functional Aspects of Genomes

Poster Abstracts

5-POS Board 5 Identifying Viral Genome Structures Throughout the Viral Life Cycle by Chemical Modification, Sequencing and Simulation Roland G. Huber 1 , Adelene Sim 1 , Yue Wan 2 , Peter J. Bond 1,3 . 1 n/a, Singapore, Singapore, 2 Bioinformatics Institute (BII), Singapore, Singapore, 3 Genome Institute Singapore (GIS), Singapore, Singapore, 4 National University Singapore (NUS), Singapore, Singapore. Viral genomes are necessarily highly dynamic, as they undergo many structural changes throughout a complex life cycle consisting of translation, replication, packaging and uncoating phases. To understand the structure and dynamics of these genomes, we apply a broad range of biophysical techniques to study local and genome-scale features of Dengue and Zika viral RNA. Recently, the envelope structures of several viruses have been determined to near-atomistic resolution using Cryo-EM. However, a detailed understanding of the viral genome arrangements still eludes us, as the genome is not as rigidly structured as the viral envelope. While it is well known that these viruses contain non-coding regulatory structural elements within their genomic RNA especially in the 5' and 3' regions, we show that the coding regions contain additional structures that are both highly conserved within and across serotypes, and these structures are functionally important for the viral life cycle. To this end, we employ chemical structure probing techniques in conjunction with next-generation sequencing, such as Shape-MaP and SPLASH, to derive information on the fold of the viral genomes at different phases in their life cycle, allowing us to accurately identify which structural elements are present at what stage. Using this information as constraints, we then proceed to use coarse-grained molecular modeling and simulation techniques to create detailed three-dimensional models that in turn allow us to understand the spatial arrangement of structural elements within the viral RNA. We proceed to integrate these results with our prior work on the structure and dynamics of the viral envelope to derive a complete model of a fully assembled, infectious virion in its mature state.

39