Fig. 2: Functional profiling of sequences involved in dimerization by mutational interference.
From: Short- and long-range interactions in the HIV-1 5′ UTR regulate genome dimerization and packaging
a, 1G, 2G and 3G capped and uncapped transcript variants migrate as distinct monomer and dimer bands on native agarose gels in both low and high salt buffers. Experiments were performed four times and representative data shown. b–f, Kdimer is a relative measure of the effects of a mutation on dimerization, calculated as the ratio of mutation frequencies in the monomer versus the dimerized RNA, and corrected for errors introduced during library preparation and sequencing. b, The log2(Kdimer) values binned according to functional domain in the 5′ UTR: TAR, U5, PBS, SL1, SL2, SL3 and SL4. None refers to nucleotide positions that do not fall into any structural domain. c,d, Median log2(Kdimer) values for each genome position for all three uncapped transcript variants in high (c) and low (d) salt buffers. Lines represent median log2(Kdimer) values smoothed with a window size of 5 nt. P, probability. e,f, The log2(Kdimer) values of the 1G and 3G transcript variants compared to the mean of the 1G, 2G and 3G transcripts in high (e) and low (f) salt buffers.
