Fig. 1: Analysis of HIV-1 dimerization.
From: Short- and long-range interactions in the HIV-1 5′ UTR regulate genome dimerization and packaging
a, Dimerization is a key step in the HIV-1 life cycle. Monomeric RNA is thought to be preferentially translated, in contrast to dimeric RNA, which is a prerequisite for packaging into virions. Dimeric RNA helps maintain genome integrity through recombination. b, The HIV-1 5′ UTR is composed of distinct structural domains linked to different functions in the HIV-1 life cycle. TAR stands for transcription. PolyA stands for polyadenylation that is inactive in the 5′ UTR. U5 in unique 5 region or PBS, stands for annealing of the host tRNA for initiating reverse transcription. SL1–SL3 contain the packaging signal. SL2 contains the splice donor site. Dimerization occurs through a kissing loop interaction at a sequence in SL1. LDIs/alternative folds involving LDIs, such as between SL1–U5 and U5–AUG may regulate dimerization. c, FARS-seq. Mutant RNA sequences are generated by mutagenic PCR and in vitro transcription. Mutant populations are physically separated into monomer and dimer fractions and probed with DMS or left untreated. Mutation frequencies are analyzed by next generation sequencing. d, Functional profiles are obtained by mutational interference. Kdimer is a quantitative measure of dimerization based on the ratio of mutations in the dimer selected versus monomer selected population, corrected for mutations introduced during the library preparation and sequencing. e, Structural profiles are obtained by DMS that specifically reacts with unpaired A and C residues. DMS-MaPseq measures DMS reactivities as mutation rates in DMS treated versus untreated controls. f, Two-dimensional analysis identifies RNA stems through correlations between stem-disrupting mutations and mutations induced by DMS.
