Fig. 3: Structural profiling identifies distinct structural conformations of the HIV-1 5′ UTR.
From: Short- and long-range interactions in the HIV-1 5′ UTR regulate genome dimerization and packaging
a, Clustering of Kendal rank correlations of DMS reactivities across all positions reveals structural relationships between monomer and dimer isolated populations from uncapped and capped transcript variants in high and low salt buffer. Relationships between sample DMS reactivities was determined by hierarchical clustering using the ‘average’ linking method. b, PCA of DMS reactivities identifies structural four structural classes of the HIV-1 5′ UTR. c, Variance in DMS reactivities across genome positions from all samples is enriched at the SL1 and TAR/polyA boundary. d, Statistical analysis of DMS reactivities in 1G/2G and 3G structural classes finds that significant differences in reactivities are mainly localized to polyA and SL1. A z-factor test identifies nucleotides where DMS reactivities change by >1.96 standard deviations of the DMS errors. An absolute difference threshold ensures that a minimum reactivity change of 0.2 is needed for the site to be considered biologically relevant. The relative threshold of 0.75-fold is used to remove false positives where DMS reactivities are high in both conditions such that a large change in reactivity is unlikely to affect RNA structure.
