Fig. 2

General properties of Zika-host RNA-RNA interactions. a Locations of interacting host RNAs on the viral genomes. Aggregate data and data classified by type of host RNA are shown. We observed differences in binding patterns by different classes of RNA along the genome. b The number of interactors in each coding region normalized by the length of the respective region. We observed the highest abundance of interactions in the NS2B-coding region. c Number of Zika genome binding sites for any specific host RNA (“Zika to host”). Most interactions bind at a specific, unique site. Promiscuous interactions of host RNA are present but considerably rarer. Inset, top: An example of a highly specific interaction between host RNA and virus genome, whereby SNORD27 only binds to a single region in ZIKV. Bottom: An example of promiscuous interaction between host RNA and virus genome whereby 7SK binds to many locations along ZIKV. d Number of interaction sites on host RNAs that bind to ZIKV genome (“host to Zika”). Data shows mostly unique interactions, but a higher propensity for 2 or more interaction sites. Inset, top: An example showing only 1 host region in ZNF485 interacting with the virus genome. Bottom: An example showing that many regions along SLC25A6 bind to the virus genome. e Sites along the Zika genome that show high numbers of interactions (99^th percentile of interactions) show a significant preference for single-stranded, high SHAPE reactivity segments inside virion particles. f Host RNAs interacting at ZIKV position 1217 with low predicted interaction energy corresponding to low observed read counts and high interaction energies coinciding with high observed read counts, indicating interaction energetics is a significant factor driving specific host-virus interactions. g Aggregate interaction energy statistics for percentiles of observed interaction counts, again with high interaction counts corresponding to high predicted interaction energy and significant differences between all classes. h Volcano plot showing the fold change in gene expression of host RNAs after 24 h of ZIKV infection. ZIKV interactors are colored as red dots, while the non-interactors are in blue. The dotted lines indicate a 1.5-fold change in gene expression