Fig. 5: KARR-seq reveals viral RNA structures and virus–host RNA–RNA interactions.

a, Loop and stripe structures across the RSV (top) and VSV (bottom) RNAs in infected A549 cells. b,c, KARR-seq arc groups for the NUCB1 (b) and EWSR1 (c) transcripts in control and RSV-infected A549 cells. Folding index: 0.415 for NUCB1 after RSV infection, 0.527 for NUCB1 without infection, 0.411 for EWSR1 after RSV infection and 0.532 for EWSR1 without infection. d, RNA folding index in control, RSV-infected and VSV-infected A549 cells. n denotes the number of chimeric read level folding index. n = 1,772,734 for no infection, n = 596,451 for RSV and n = 159,725 for VSV. The lower and the upper bounds denote 25th and 75th percentiles, respectively. The minima denote the lower bound −1.5× IQR. The maxima denote the upper bound +1.5× IQR. P values were calculated by the two-sided Mann–Whitney test. e,f, The number of host RNAs from each RNA category that interact with RSV (e) and VSV (f) RNAs. g, Fluorescent imaging of GFP-tagged RSV and GFP-tagged VSV after cells were transfected with denoted LNA ASOs. These ASOs target mRNA transcripts at positions that interact with RSV RNA. Scale bar, 100 µm. h,i, The percentage of RSV-positive (h) and VSV-positive (i) cells quantified by flow cytometry after cells were treated with denoted LNA ASOs. Data are mean ± s.d. n = 3 biologically replicates. P values were calculated by two-tailed Student’s t-test. IQR, interquartile range.