Extended Data Fig. 8: Pseudouridine in piRNAs and tRNA fragments (tRFs) from mouse testis.
From: Pseudouridine guides germline small RNA transport and epigenetic inheritance
(a, b) Ψ detection by Ψ-IP (a) and CMC-depletion (b) of small RNA from testes of 8 weeks-old male mice. Dots correspond to tRF counts per tRNA isoacceptor. Differential expression (fold change) and statistical significance were calculated using the DESeq2 package61. Statistically significant (p-adj. <0.01, log2 fold change > |1|) enriched or depleted tRFs are in black, 3’-tRFs are colored blue; grey dots mark tRFs without significant enrichment/depletion. (c) Volcano plot of read counts per piRNA sequence in testes (8 weeks old males) by CMC-depletion and sequencing. Black: significant fold changes (p-adj. <0.01, log2 fold change > |1|) as per DESeq2 analysis; grey: not significant; blue: significantly enriched or depleted piRNAs overlapping LTR and LINE transposon sequences. (d) Volcano plot of read counts per piRNA sequence by Ψ-IP. Black: significant fold changes (p-adj. <0.01, log2 fold change > |1|) as per DESeq2 analysis; grey: not significant; blue: significantly enriched or depleted piRNAs overlapping LTR and LINE transposon sequences. (e,f) Volcano plot of read counts per piRNA cluster using Ψ-IP (e) or CMC-depletion (f) and DESeq2 for statistical analysis. (g,h) Size distribution of 3’-tRFs (g) and piRNA (h) sequences (without structural RNAs) using CMC-depletion and sequencing. (i, j) Size distribution of 3’-tRFs (i) and piRNA (j) sequences (without structural RNAs) using Ψ-IP and sequencing. RPM: reads per million mapped reads.
