Fig. 6

Pachytene piRNA biogenesis is phased in mice. a U bias at position +1 downstream of piRNA 3′ ends in Pnldc1 ^Mut total piRNA. The 24–48 nt reads from WT and Pnldc1 ^Mut (Mut-1) total piRNA libraries were mapped to one representative pachytene piRNA cluster (2-qE1-35981.1, the most abundantly expressed). Sequence logos showing nucleotide composition at mapped piRNA 5′ ends, 3′ ends, and downstream regions of 3′ ends were generated. Gray shading marks the piRNA region. b U bias at position +1 downstream of piRNA 3′ end in Pnldc1 ^Mut MILI-piRNAs and MIWI-piRNAs. The 24–48 nt reads from WT and Pnldc1 ^Mut (Mut-1) MILI- and MIWI-piRNA libraries were mapped to one representative pachytene piRNA cluster (2-qE1-35981.1). Sequence logos showing nucleotide composition in the vicinity of mapped piRNA 3′ ends were generated. Gray shading marks the piRNA region. c Untrimmed Pnldc1 ^Mut piRNAs exhibit coupling of piRNA 3′ ends with subsequent piRNA 5′ ends. The 24–48 nt reads from WT and Pnldc1 ^Mut (Mut-1) total piRNA libraries were mapped to one representative pachytene piRNA cluster (2-qE1-35981.1). Top 1000 distinctively mapped piRNAs were extracted as references to perform 3′–5′ coupling analysis. The frequency of piRNA 5′ ends around referenced piRNA 3′ ends was calculated. Z-scores at position +1 (Z1) are shown