Heterogeneity of chromatoid bodies in adult pluripotent stem cells of planarianDugesia japonica

Planarian PIWI-piRNA Interaction Analysis Using Immunoprecipitation and piRNA Sequencing

The freshwater planarian Dugesia japonica is a good in vivo model for studying the function of piwi genes in adult pluripotent stem cell (aPSC) due to their abundant aPSCs. Generally, PIWI family proteins encoded by piwi genes bind to small noncoding RNAs called piRNAs (PIWI-interacting piRNAs). The analysis of PIWI-piRNA complexes in the planarian is useful for revealing the functions of piwi genes in the aPSC system. In this chapter, we present an immunoprecipitation protocol for PIWI-piRNA complexes from whole planarians.

The piRNA pathway in planarian flatworms: new model, new insights

PIWI-interacting RNAs (piRNAs) are small regulatory RNAs that associate with members of the PIWI clade of the Argonaute superfamily of proteins. piRNAs are predominantly found in animal gonads. There they silence transposable elements (TEs), regulate gene expression and participate in DNA methylation, thus orchestrating proper germline development. Furthermore, PIWI proteins are also indispensable for the maintenance and differentiation capabilities of pluripotent stem cells in free-living invertebrate species with regenerative potential. Thus, PIWI proteins and piRNAs seem to constitute an essential molecular feature of somatic pluripotent stem cells and the germline. In keeping with this hypothesis, both PIWI proteins and piRNAs are enriched in neoblasts, the adult stem cells of planarian flatworms, and their presence is a prerequisite for the proper regeneration and perpetual tissue homeostasis of these animals. The piRNA pathway is required to maintain the unique biology of planarians because, in analogy to the animal germline, planarian piRNAs silence TEs and ensure stable genome inheritance. Moreover, planarian piRNAs also contribute to the degradation of numerous protein-coding transcripts, a function that may be critical for neoblast differentiation. This review gives an overview of the planarian piRNA pathway and of its crucial function in neoblast biology.

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

Planarians have a remarkable regenerative ability owing to their adult pluripotent stem cells (aPSCs), which are called "neoblasts." Planarians maintain a considerable number of neoblasts throughout their adulthood to supply differentiated cells for the maintenance of tissue homeostasis and asexual reproduction (fission followed by regeneration). Thus, planarians serve as a good model to study the regulatory mechanisms of in vivo aPSCs. In asexually reproducing invertebrates, such as sponge, Hydra, and planaria, piwi family genes are the markers most commonly expressed in aPSCs. While piwi family genes are known as guardians against transposable elements in the germline cells of animals that only sexually propagate, their functions in the aPSC system have remained elusive. In this review, we introduce recent knowledge on the PIWI family proteins in the aPSC system in planarians and other organisms and discuss how PIWI family proteins contribute to the regulation of the aPSC system.

Planarians recruit piRNAs for mRNA turnover in adult stem cells

In this study, Kim et al. set out to elucidate the molecular details of how PIWI proteins in planarian flatworms contribute to stem cell function and regeneration. Using novel biochemical tools, such as IP-seq, ribodepletion, HITS-CLIP, and SHAPE-MaP, the authors show that PIWI proteins enable planarians to repurpose piRNAs for critical roles in neoblast mRNA turnover.

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.

Planarian Stem Cell Heterogeneity

Planarian (Platyhelminthes, Triclads) are free-living flatworms endowed with extraordinary regenerative capabilities, i.e., the ability to rebuild any missing body parts also from small fragments. Planarian regenerative capabilities fascinated scientific community since early 1800, including high-standing scientists such as J.T. Morgan and C. M. Child. Today, it is known that planarian regeneration is due to the presence of a wide population of stem cells, the so-called neoblasts. However, the understanding of the nature of cells orchestrating planarian regeneration was a long journey, and several questions still remain unanswered. In this chapter, beginning from the definition of the classical concept of neoblast, we review progressive discoveries that have brought to the modern view of these cells as a highly heterogeneous population of stem cells including pluripotent stem cells and undifferentiated populations of committed progenies.

PIWI-piRNA pathway: Setting the pace of aging by reducing DNA damage

Transposable elements (TEs) are powerful drivers of genome evolutionary dynamics but are principally deleterious to the host organism by compromising the integrity and function of the genome. The transposition of TEs may result in mutations and DNA damage. DNA double-strand breaks (DSBs), which may be caused by the transposition, are one of the processes directly linked to aging. TEs may thus be considered to constitute an internal source of aging and the frequency of transposition may, in turn, be considered to affect the pace of aging. The PIWI-piRNA pathway is a widespread strategy used by most animals to effectively suppress transposition. Interestingly, the PIWI-piRNA pathway is expressed predominantly in the animal germline, a more or less continuous immortal lineage set aside after the first few cell divisions of a developing embryo. Recent findings further imply that the PIWI-piRNA pathway and TE suppression constitute an important mechanism regulating aging. This article discusses the proposed role of the PIWI-piRNA pathway in setting the pace of aging as well as the possible mechanisms underlying this process.

Girardia dorotocephala transcriptome sequence, assembly, and validation through characterization of piwi homologs and stem cell progeny markers

Planarian flatworms are popular models for the study of regeneration and stem cell biology in vivo. Technical advances and increased availability of genetic information have fueled the discovery of molecules responsible for stem cell pluripotency and regeneration in flatworms. Unfortunately, most of the planarian research performed worldwide utilizes species that are not natural habitants of North America, which limits their availability to newcomer laboratories and impedes their distribution for educational activities. In order to circumvent these limitations and increase the genetic information available for comparative studies, we sequenced the transcriptome of Girardia dorotocephala, a planarian species pandemic and commercially available in North America. A total of 254,802,670 paired sequence reads were obtained from RNA extracted from intact individuals, regenerating fragments, as well as freshly excised auricles of a clonal line of G. dorotocephala (MA-C2), and used for de novo assembly of its transcriptome. The resulting transcriptome draft was validated through functional analysis of genetic markers of stem cells and their progeny in G. dorotocephala. Akin to orthologs in other planarian species, G. dorotocephala Piwi1 (GdPiwi1) was found to be a robust marker of the planarian stem cell population and GdPiwi2 an essential component for stem cell-driven regeneration. Identification of G. dorotocephala homologs of the early stem cell descendent marker PROG-1 revealed a family of lysine-rich proteins expressed during epithelial cell differentiation. Sequences from the MA-C2 transcriptome were found to be 98-99% identical to nucleotide sequences from G. dorotocephala populations with different chromosomal number, demonstrating strong conservation regardless of karyotype evolution. Altogether, this work establishes G. dorotocephala as a viable and accessible option for analysis of gene function in North America.

DjPiwiB: A Rich Nuclear Inheritance for Descendants of Planarian Stem Cells

Stem cell differentiation involves a delicate balance of gene expression and transposon repression. In this issue of Developmental Cell, Shibata et al. (2016) show that a PIWI protein expressed in planarian stem cells is inherited by their differentiating descendants to ensure regenerative capacity of the flatworm via transposon silencing.