Extended Data Fig. 2: High encoding specificity of RCE strategy verified by the limited off-target Ψ edits as well as low off-target Ψ editing ratios across the transcriptome.
From: RNA codon expansion via programmable pseudouridine editing and decoding
a, Complementary regions between gsnoRNA (black) and target site in SrcK295TGA-GFP reporter (blue). b, Complementary regions between gsnoRNA (black) and an off-target site in the endogenous gene (red). c, Sequence motif of the RCE-induced off-target Ψ sites. d, The on-target and off-target regions within the secondary structure of the gsnoRNA-Src predicted by RNAfold. The base-pair probabilities are indicated with color. Red and blue colors represent high and low probabilities, respectively. e,f IGV views representing the reads mapped at the off-target sites in 3’ UTRs of NM_001032283.3(e) and XM_017027173.2(f). g, Pie chart showing the distribution of RCE-induced off-target Ψ sites in the transcriptome. h, Scatterplot showing the expression level of genes containing the off-target Ψ sites by RNA-seq. Data are represented as the mean values (n = 2 biologically independent replicates). i, Scatterplot showing the translation level of genes containing the off-target Ψ sites by Ribo-seq. Data are represented as the mean values (n = 2 biologically independent replicates). The correlations between different conditions were measured via Pearson’s correlation score by defaulted parameters.
