Extended Data Fig. 2: Identification of known and novel rRNA sites under DKC1 knockdown and evaluation of the deletion rate for other RNA modifications.
From: Quantitative profiling of pseudouridylation landscape in the human transcriptome
(a) An IGV view of read mapping showing deletion signals in position 1840–1860 of 28S rRNA. Two deletion sites were marked between four consecutive Ts in 1847–1850. (b) Boxplot representing the relative mRNA expression level of shControl and shDKC1 samples detected by qPCR. n = 2 biological replicates. (c) The protein expression level of DKC1 knock-down cells was determined by Western blot. GAPDH was used as a loading control. (d) Heatmap of deletion rates of all Ψ sites in 5.8S rRNA, 18S rRNA and 28 rRNA between shControl and shDKC1 sample. (e) Deletion rate of three additional Ψ sites in rRNA in shControl and shDKC1 sample. Each sites have two replicates of shControl and shDKC1 sample. (f) Deletion rate of treated and untreated samples on known Ψm and m1acp3Ψ sites in rRNA. (g) Deletion rate of treated and untreated samples on known Am (n = 34), Cm (n = 24), Gm (n = 32), and Um (n = 19) sites in rRNA. Error bars represent mean ± SD. (h) Deletion rate of treated and untreated samples on known m62A, m6A, m1A, ac4C, and m5C sites in rRNA.
