Planarians recruit piRNAs for mRNA turnover in adult stem cells

Abstract

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. Thus, PIWI proteins enable planarians to repurpose piRNAs for potentially critical roles in neoblast mRNA turnover.

What is the role of PIWI family proteins in adult pluripotent stem cells? Insights from asexually reproducing animals, planarians

“…Genes in Piwi-2/B are transcriptionally expressed in neoblasts and brain neurons, and code for nuclear PIWIs (Almazan et al, 2018;Kim et al, 2019;Nakagawa et al, 2012;Reddien, Oviedo, Jennings, Jenkin, & Sánchez Alvarado, 2005;Shibata et al, 2016;Zeng et al, 2013). Meanwhile, genes in Piwi-3/C are transcriptionally expressed in neoblasts and brain neurons and code for cytoplasmic PIWIs localized in CBs (Kashima, Kumagai, Agata, & Shibata, 2016;Kim et al, 2019;Palakodeti et al, 2008;Rouhana, Vieira, Roberts-Galbraith, & Newmark, 2012). The PIWI-3/C group is similar to PIWIs in other animals, especially AGO3 in the fly and MILI in the mouse (Figure 3) (Nakagawa et al, 2012;Palakodeti et al, 2008).…”

“…SMEDWI-1 protein is a cytoplasmic PIWI observed in neoblasts and early neoblast progeny during the course of differentiation, although Smedwi-1 mRNA is expressed only in the neoblasts as well as in D. japonica (Guo et al, 2006). SMEDWI-2 are nuclear PIWIs existing in both the neoblasts and differentiated cells similar to DjPiwiB in D. japonica (Kim et al, 2019;Wang et al, 2019;Zeng et al, 2013); thus, suggesting that SMEDWI-2 might also be inherited by somatic descendants from the neoblasts. SMEDWI-3 is a cytoplasmic PIWI and a component of CB (Kim et al, 2019;Rouhana et al, 2012).…”

“…Genes in Piwi-1/A are transcriptionally expressed specifically in neoblasts and code for cytoplasmic PIWIs (Almazan, Lesko, Markey, & Rouhana, 2018;Guo et al, 2006;Nakagawa, Ishizu, Hasegawa, Kobayashi, & Matsumoto, 2012;Yoshida-Kashikawa et al, 2007). Genes in Piwi-2/B are transcriptionally expressed in neoblasts and brain neurons, and code for nuclear PIWIs (Almazan et al, 2018;Kim et al, 2019;Nakagawa et al, 2012;Reddien, Oviedo, Jennings, Jenkin, & Sánchez Alvarado, 2005;Shibata et al, 2016;Zeng et al, 2013). Meanwhile, genes in Piwi-3/C are transcriptionally expressed in neoblasts and brain neurons and code for cytoplasmic PIWIs localized in CBs (Kashima, Kumagai, Agata, & Shibata, 2016;Kim et al, 2019;Palakodeti et al, 2008;Rouhana, Vieira, Roberts-Galbraith, & Newmark, 2012).…”

Efficient depletion of ribosomal RNA for RNA sequencing in planarians

“…This could be due to 253 their similar sequencing depth compared to the other polyA libraries. The transcripts whose 254 abundance was most significantly affected by poly(A) selection were found to be histone mRNAs that 255 are known to lack polyA tails ( Figure 3G our rRNA depletion workflow also allows for the detection of transposable element degradation 265 products that were generated by PIWI proteins guided by specific piRNAs, an abundant class of small 266 RNAs in planarians [39,40]. 267 268…”

“…Raw sequencing reads for planarian rRNA-depleted dataset were downloaded from the project 377 GSE122199 (GSM3460490, GSM3460491, GSM3460492). The libraries were prepared as described 378 [40]. Briefly, planarian rRNA depleted RNA-Seq libraries were prepared from 100,000 FACS-sorted 379 planarian X1 cells as described [ Separation profile of total RNA before and after rRNA depletion.…”