Developmentally regulated piRNA clusters implicate MILI in transposon control

Nearly half of the mammalian genome is composed of repeated sequences. In Drosophila, PIWI proteins exert control over transposons. However, mammalian PIWI proteins, Miwi and Mili, partner with piRNAs that are depleted of repeat sequences, raising questions about a role for mammalian PIWIs in transposon control. A search for murine small RNAs that might program PIWI proteins for transposon suppression revealed developmentally regulated piRNA loci, some of which resemble transposon master control loci of Drosophila. We also find evidence of an adaptive amplification loop in which PIWI catalyzes formation of piRNA 5’ ends. Mili mutants de-repress L1 and IAP and lose DNA methylation of L1 elements, demonstrating an evolutionarily conserved role for PIWI proteins in transposon suppression. Keywords: small RNA profile, piRNA Mili RNP complexes were immunoprecipitated from testes extract of 10 day old CD-1 mice using polyclonal antibodies against two MILI peptides (MILI-N, amino acids 2-18 and MILI-N2, amino acids 107-122). Immunoprecipitation of MILI RNP complexes and RNA isolation was performed as described in A. Aravin et al., Nature 442, 203 (2006). Two cDNA libraries were created and sequenced separately. After preliminary analysis, sequences were pooled. Small RNA cloning and 454 sequencing of small cDNA libraries were performed as described in J. Brennecke et al., Cell 128, 1089 (2007).