T-hairpin structure found in the RNA element involved in piRNA biogenesis

PIWI-interacting RNAs (piRNAs) repress transposons to protect the germline genome from DNA damage caused by transposon transposition. In Drosophila , the Traffic jam ( Tj ) mRNA is consumed to produce piRNA in its 3′-UTR. A cis element located within the 3′-UTR, Tj-cis , is necessary for piRNA biogenesis. In this study, we analyzed the structure of the Tj-cis RNA, a 100-nt RNA corresponding to the Tj-cis element, by the SHAPE and NMR analyses and found that a stable hairpin structure formed in the 5′ half of the Tj-cis RNA. The tertiary structure of the 16-nt stable hairpin was analyzed by NMR, and a novel stem–loop structure, the T-hairpin, was found. In the T-hairpin, four uridine residues are exposed to the solvent, suggesting that this stem–loop is the target of Yb protein, a Tudor domain-containing piRNA biogenesis factor. The piRNA biogenesis assay showed that both the T-hairpin and the 3′ half are required for the function of the Tj-cis element, suggesting that both the T-hairpin and the 3′ half are recognized by Yb protein.