Characterization of the RNA present in L1 ORF1p macromolecular complexes from Mael-/- mouse testes

piRNA-deficient Maelstrom (Mael) null mice are characterized by a strong upregulation of LINE-1 (L1) retrotransposon in meiotic spermatocytes. This defect turns out in the accumulation of L1 RNA and ORF1p in their cytoplasm and the formation of prominent ribonucleoprotein aggregates. We used 3-months-old Mael-/- male mice to characterize the RNA present in those ORF1p aggregates. To favor the isolation of complexed versus free ORF1p protein, we first fractionated Mael-/- testis extracts (that we refer to as TOTAL) by sucrose gradient ultracentrifugation, in the presence of EDTA. We then pooled the sucrose fractions where ORF1p macromolecular complexes sediment (fractions 5-8) and used this pool as the INPUT for an anti-ORF1p co-immunoprecipitation (IP) followed by RNA-seq. Enrichment of RNAs in anti-ORF1p co-immunoprecipitation samples (IP) was calculated over the background controls (Beads Only - BO), over the pools of sucrose fractions 5-8 (INPUT), and over the testis extracts originally loaded on sucrose gradients (TOTAL). Three biological replicates are reported.