Fig. 3: The 22-bulge governs the accuracy and efficiency of DICER cleavage at DC21.
From: Secondary structure RNA elements control the cleavage activity of DICER
a The cleavage efficiency and accuracy scores of DICER in the HT cleavage assays. Density plots of DC21 and DC22 are shown in blue and grey, respectively. b The 22-bulge-containing structures (structures 20 and 29) exhibited the highest cleavage accuracy and efficiency at DC21. c The cleavage accuracy scores of DICER in shRNAs containing different structures. d–f Line graphs to show the log2(DC21/other DC) (d), cleavage efficiency score at DC21 (e), and log2(DC/SC) (f) of variants containing: 22-bulge 3p (22-B 3p), 22-loop (22-L), 22-single mismatch (22-mM), or 22-bulge 5p (22-B 5p). The p-values were calculated by two-sided Wilcoxon rank-sum tests. g The structures and sequences of shRNAs. h The in vitro DICER cleavage assays for RNAs in (g). i The cleavage accuracy of DICER in (h) was calculated as a ratio of the cleaved product at a certain position to those at other positions. j The cleavage efficiency of DICER in (h) was calculated as a ratio of the cleaved product at DC21 or DC22 to the original substrate, n = 3 independent experiments. A two-tailed t-test calculated the p-values. The error bars were presented with 95% confidence intervals. k, l The cleavage accuracy and efficiency scores of the 22-bulge variants containing different nt in the bulge. m The base-pairing probabilities of different nt in 22-bulge generated by RNAfold62. The positional base-pairing probability of a variant was calculated as the ratio of the number of structures containing a base-pair at a specific position to the total number of predicted structures. In (k–m), The number of variants for each nt: n = 43 (A); n = 39 (U); n = 31 (C); n = 17 (G). The center line is median, the lower and upper bounds of the box are the 25th and 75th percentiles, whiskers show 1.5x the interquartile extending from bounds of box, minima is the minimum value, and maxima is the maximum value. Individual data values are shown as dots. Source data are provided as a Source Data file.
