Fig. 2.

LUC transgene expression is inversely correlated with RSS of 3′ UTRs. a Predicted base-pairing probabilities of the 3' UTRs for different transgene lines (P_CHR2-LUC-3′ UTR, P_CHR2-LUC-pri-miR159a-3′ UTR, P_CHR2-LUC-pri-miR159a-T1-3′ UTR, P_CHR2-LUC-pri-miR159a-T1-1-3′ UTR, and P_CHR2-LUC-pri-miR164a-3′ UTR) via RNAstructure [23]. P values by Wilcoxon test. b Schematic pipeline of 3′ end target-specific DMS-MaPseq for both in vivo and in vitro conditions. See Methods for details. GSP, gene specific primer; TGIRT, thermostable group II intron reverse transcriptase. c, d RSS of the 3′ UTRs for different transgene transcripts in a. The DMS signals of A and C residues were color-coded and U/G bases were marked in gray. Quantification of luminescence results of the representative samples was shown in the right part. LUC pictures in c and d were taken under different CCD cameras, with each experiment having its own CK (P_CHR2-LUC-3′ UTR) lines. Whiskers represent the minimum and maximum values whereas horizontal lines in the boxplots display the 75^th, 50^th, and 25^th percentiles, respectively. Statistical test was performed between different transgenic lines and P_CHR2-LUC-3′ UTR. ns, no significance; *P < 0.05; **P < 0.01; ***P < 0.001; unpaired two-tailed Student’s t test. e–f Gini index of in vivo (e) and in vitro (f) DMS reactivities of the 3′ UTRs for different transgene lines. P values by Wilcoxon test. In a, e, and f, horizontal lines in the boxplots display the 75^th, 50^th, and 25^th percentiles, respectively. The upper fence is 75^th percentile + 1.5 * interquartile range. The lower fence is 25^th percentile − 1.5 * interquartile range. Dots represent the outliers