Fig. 4: Massively parallel quantification of the RNP interactome using the RNA structure library.

a Schematic of the RNA pull-down assay with the RNA structure library, version 1. The numbers of target RNA structures are described in parentheses. b FOREST analysis of let-7 loops using RNA structure library, version 1 (1916 structures). The known let-7 loops were categorized into three subclasses according to the presence of a cold-shock domain (CSD)-binding site and a zinc knuckle domain (ZKD)-binding site. The X-axis indicates the binding intensity of His-tagged LIN28A recombinant protein. The error bars indicate means ± s.d. of multiple barcodes assigned to each RNA. The additional lines indicate the top intensity, Z-score = 2.0, and mean. Binding intensities were calculated from the results of two independent experiments. The multiple alignments are taken from a previous study²¹. c Gel image of EMSA using 50 nM RNA. LIN28A solution was prepared by adjusting the concentration to 0, 200, 400, or 600 nM. The image shows representative data from three independent experiments. Source data are provided as a Source Data file. d The bar plots represent the band shift ratios observed in (c). The error bars indicate means ± s.e.m. The experiments were performed with three biological replicates. The p-values were determined by two-tailed Dunnett’s test. ***p < 0.001, **p < 0.01, *p < 0.05. n.d. indicates no significant difference. Each “×” indicates a data point. e Average LIN28A-binding intensities of let-7 class-1 and class-2. We omitted the score of the hsa-let-7f-2 loop from the calculation because it did not show a high intensity, unlike other class-2 loops. The numbers of analyzed let-7 loops are described in parentheses. The error bars indicate means ± s.e.m., and the p values were determined by two-tailed t tests. Each “×” indicates a data point.