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 (PCHR2-LUC-3′ UTR, PCHR2-LUC-pri-miR159a-3′ UTR, PCHR2-LUC-pri-miR159a-T1-3′ UTR, PCHR2-LUC-pri-miR159a-T1-1-3′ UTR, and PCHR2-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 (PCHR2-LUC-3′ UTR) lines. Whiskers represent the minimum and maximum values whereas horizontal lines in the boxplots display the 75th, 50th, and 25th percentiles, respectively. Statistical test was performed between different transgenic lines and PCHR2-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 75th, 50th, and 25th percentiles, respectively. The upper fence is 75th percentile + 1.5 * interquartile range. The lower fence is 25th percentile − 1.5 * interquartile range. Dots represent the outliers