Planarians recruit piRNAs for mRNA turnover in adult stem cells

PIWI proteins utilize small RNAs called piRNAs to silence transposable elements, thereby protecting germline integrity. In planarian flatworms, PIWI proteins are essential for regeneration, which requires adult stem cells termed neoblasts. Here, we characterize planarian piRNAs and examine the roles of PIWI proteins in neoblast biology. We find that the planarian PIWI proteins SMEDWI-2 and SMEDWI-3 cooperate to degrade active transposons via the ping-pong cycle. Unexpectedly, we discover that SMEDWI-3 plays an additional role in planarian mRNA surveillance. While SMEDWI-3 degrades numerous neoblast mRNAs in a homotypic ping-pong cycle, it is also guided to another subset of neoblast mRNAs by antisense piRNAs and binds these without degrading them. Mechanistically, the distinct activities of SMEDWI-3 are primarily dictated by the degree of complementarity between target mRNAs and antisense piRNAs. Planarian PIWI proteins thus act as both nucleases and RNA-binding proteins, enabling planarians to repurpose piRNAs for critical roles in neoblast mRNA turnover. Overall design: RNA-Seq, small RNA-Seq and Degradome-Seq libraries were prepared in triplicates. CLASH-Seq and HITS-CLIP have in total 9 replicates of separately prepared and sequenced libraries from up and down CLIP signal band. RNAi knockdown of smedwi-2 and smedwi-3 were carried out by feeding worms with dsRNA. As a control planarians were fed with dsRNA of unc-22 (C. elegans). For SHAPE-map total RNA was treated with 20 mM of 1M7 in DMSO or neat DMSO (as a negative contol). CHIP-Seq libraries were prepared in duplicates. Each replicate of CHIP-Seq libraries was sequenced on four lanes (four FASTQ files per sample). Please note that the CLASH_and_CLIP_counts.txt.gz contains 9 (weighted counts from merged and jointly processed) data columns generated from the following sample raw data as described below: hitsclip1 - GSM3704066 and GSM3704067 hitsclip2 - GSM3460485 and GSM3460488 hitsclip3 - GSM3460486 and GSM3460489 clash 1-6 - GSM3704054 to GSM3704065