Fig. 3: Translation suppresses mRNA higher-order structures under native and stress conditions.

a, The effect of ribosome binding on RNA–RNA interactions in HepG2 cells. The x axis denotes ribosome binding strength, and the y axis shows the folding index difference between in vitro and in vivo. b, KARR-seq arc groups for the NCL transcript in control and harringtonine-treated HepG2 cells. Folding index: 0.246 for control and 0.290 for harringtonine. c, Metagene plot showing the relative abundance of intermolecular mRNA interactions under denoted conditions. CHX, cycloheximide; HT, harringtonine. d, The transcriptome-wide distribution of beta coefficients under denoted conditions. *** indicates P < 0.001. e, Folding index for mRNA and lncRNA in control and harringtonine-treated HepG2 cells. f, The length of transcripts that exhibit upregulated and downregulated intramolecular interactions after arsenite treatment in K562 cells. g, The 5′ UTR, CDS and 3′ UTR length for mRNAs that exhibit upregulated and downregulated intramolecular interactions after arsenite treatment in K562 cells. h, The translation efficiency under the normal condition for mRNAs that exhibit upregulated and downregulated intramolecular interactions after arsenite treatment in K562 cells. In f–h, for the analysis of all transcripts, n = 104 transcripts for the downregulated group and n = 73 transcripts for the upregulated group. For the analysis of mRNAs, n = 102 transcripts for the downregulated group and n = 68 transcripts for the upregulated group. i, mRNA folding index in control, arsenite-treated and harringtonine-treated K562 cells and purified K562 nuclei. n refers to the number of chimeric read level folding index. n = 440,484 for whole cell control, n = 242,268 for whole cell arsenite, n = 251,601 for whole cell HT, n = 154,797 for nuclear control and n = 162,507 for nuclear arsenite. j, mRNA folding index for SG-localized transcripts and other (non-SG) transcripts in control and arsenite-treated K562 cells. n = 161 transcripts in the non-SG group and n = 215 transcripts in the SG group. For f–h, P values were calculated by the one-sided Mann–Whitney test. For e,i,j, P values were calculated by the two-sided Mann–Whitney test. In box plots shown in e–h, the lower and the upper bounds denote 25th and 75th percentiles, respectively. The minima denote the lower bound −1.5× IQR. The maxima denote the upper bound +1.5× IQR. KARR-seq was performed in two biological replicates. IQR, interquartile range.