Association with PrLD-containing RBPs preferentially decreases UPA-seq reads. (A) Scatter plot illustrating the relationship between the total number of eCLIP peaks mapped on each transcript and the fold change of reads upon UV irradiation. Blue line represents the regression line. (B) Cumulative distribution of lncRNAs that possessed high (top 25% quintile, red), middle (25–75 percentile, blue), and low (bottom 25% quintile, green) total eCLIP peaks for each RBP along the fold change of reads upon UV irradiation. Note that lncRNAs with higher total eCLIP peaks tend to be represented in a group that is less sensitive to UV irradiation. (C) Cumulative distribution of lncRNAs bound by a series of RBPs shown in D along with the fold change of reads upon UV irradiation. Note that each RBP contributes differentially to the decreased UPA-seq reads upon UV irradiation. (D) Bar plots illustrating the fold change of reads mapped to lncRNAs at the median targeted by the indicated RBPs. The magenta color represents the name of the RBPs containing a PrLD. (E) Violin and quasi-random beeswarm plots showing the fold change of reads mapped to lncRNAs at the median targeted by RBPs without PrLD (non-PrLD) and with PrLD (PrLD). Bar plots indicate the mean ± SD of fold change values shown in each category. (F) RT-qPCR quantification of specific lncRNAs indicated at the top of each panel from UV-irradiated (UV+) and nonirradiated (UV−) cells pretreated with control DMSO (cont), 1,6-hexanediol (1,6-Hex), and 2,5-hexanediol (2,5-Hex). The 2,5-hexanediol treatment suppressed the reduction of recovery from the aqueous phase upon UV irradiation. The reversed y-axes represent the Δ Cq values of each lncRNA relative to GAPDH. Bar plots indicate the mean ± SD of three biological triplicates. (G) Point plots of the P-values shown in F, as calculated by Welch's t-test.
