Effects of IDR processing in WAGO-1 and WAGO-3 on small RNA binding and overall small RNA landscapes

We carried out small RNA sequencing in different C. elegans strains with mutations of the WAGO-1 and WAGO-3 IDR processing proteases app-1 and dpf-3. Additionally, we carried out RNA immunoprecipitation sequencing (RIP-Seq) of tagged versions of WAGO-1 and WAGO-3 with or without deletions to their IDRs. Because deletion of either IDR is lethal, but full deletions of the proteins are not, all strains used for RIP-Seq carried and auxin-inducible degron and were grown on auxin plates until 4 hours before harvest. All sequencing libraries were treated with RppH to enrich for 22G RNAs.