Extended Data Fig. 5: RBRP complements the existing diazirine-based profiling method.
From: Pervasive transcriptome interactions of protein-targeted drugs
a, Chemical structure of diazirine-conjugated analogue of Levofloxacin (Lev-diazirine). The drug moiety is coloured blue, “click” handle” is coloured red, and diazirine moiety is coloured brown. b, Workflow for profiling RNA targets of Lev with Lev-diazirine probe. c, Volcano plot showing transcripts that are confidently enriched by Lev-diazirine in HEK293 cells. d, Volcano plot showing shared RNA targets that are identified by both Lev-AI and Lev-diazirine. X-axis: log-transformed ratio of transcript abundance in the presence over the absence of unmodified drug. Y-axis: the negative value of log-transformed P-value calculated with DESeq2. d, Venn diagram comparing RNA targets that were identified by Lev-AI and Lev-diazirine. e. Volcano plot showing shared transcripts (“hits”) identified by both RBRP and the existing diazirine-based profiling method. Transcripts that were enriched by Lev-diazirine are coloured grey. Shared transcripts that were identified by both Lev-AI and Lev-diazirine are coloured red. For c and e, X-axis: log-transformed ratio of transcript abundance in the presence over the absence of unmodified drug. Y-axis: the negative value of log-transformed P-value calculated with DESeq2 using a two-tailed Wald test. Fold-change=transcript abudance (Lev-diazirine-treated)/transcript abudance (Lev-diazirine + Competitor). f, Floating bar graphs comparing the distribution of RT stops of Lev-AI and Lev-diazirine towards four nucleotides. The floating bars represent the range of all data points (minimum to maximum). Lines represent the mean values. Data points are collected from two biologically independent sequencing experiments. All data points for nucleotide in each experiment are compiled for data analysis. Lev-diazirine: n = 22,958 (A), 19,154 (U), 19,375 (C), and 18,992 (G). Lev-diazirine + Competitor: n = 2,420 (A), 1,778 (U), 2,160 (C), and 1,895 (G). Lev-AI: n = 425,366 (A), 389,020 (U), 352,821 (C), and 380,397 (G). Lev-AI + Competitor: n = 423,930 (A), 389,653 (U), 354,014 (C), and 377,073 (G).
