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. Author manuscript; available in PMC: 2023 Feb 3.
Published in final edited form as: Mol Cell. 2022 Jan 19;82(3):645–659.e9. doi: 10.1016/j.molcel.2021.12.023

Figure 3. Pseudouridines are enriched in RNA binding protein binding sites.

Figure 3.

a) Genome browser views of U2AF2 and b) SF3A3 eCLIP peaks and size-matched input controls (SMI) on IDH1 and ITIH3 respectively. The location of pseudouridine relative to the eCLIP peak is denoted by (Ψ). c) Volcano plots of pseudouridines overlapping RBP eCLIP peaks displaying the fold enrichment (IP over size matched input) versus the SMI-normalized adjusted p-value (Van Nostrand et al. 2016 Nat Methods). The overlap between eCLIP peaks and pseudouridines is shown for two RBPs U2AF2 and SF3A3. Proximal introns refer to intronic sequences <500 nt from splice sites and distal introns refer to intronic sequences >500 nt from splice sites. d) Z-scores were generated by comparing the fraction of eCLIP peaks overlapping pseudouridines to the calculated overlap after shuffling pseudouridines within intronic regions 1000 times. e) The z score of pseudouridines shuffled 1000 times within intronic regions plotted against the z score of uridines shuffled 1000 times within intronic regions.