Small RNAs regulate stem cell function and regeneration in the planarian

The planarian Schmidtea mediterranea can regenerate all lost body tissue after amputation due to a population of pluripotent somatic stem cells called neoblasts, and is therefore an excellent model organism to study the roles of small RNAs in stem cell function. Here, we use a combination of deep sequencing and bioinformatics to discover 66 new miRNAs in S. mediterranea. We also identify 21 miRNAs that are specifically expressed in either sexual or asexual animals. Finally, we identified five miRNAs whose expression is sensitive to γ-irradiation, suggesting they are expressed in neoblasts or early neoblast progeny. Further analysis the deep sequencing data from fluorescence activated cell sorted (FACS) cell populations confirms that these miRNAs are expressed in neoblasts and also identified several miRNAs that are specifically expressed in differentiated cells. Together, these results increase the known repertoire of S. mediterranea small RNAs and identify numerous regulated miRNAs that may play important roles in regeneration, homeostasis, neoblast function, and reproduction. ^ In spite of miRNAs, a novel class of small RNAs called PIWI associated RNAs (piRNAs) is to preserve the integrity of the germline genome by silencing transposons, though they also participate in epigenetic and post-transcriptional gene regulation. PIWI proteins are expressed in germ cells in a wide variety of metazoans, where they participate in piRNA synthesis. In the planarian S. mediterranea, the PIWI proteins SMEDWI-1 and SMEDWI-2 are expressed in neoblasts and SMEDWI-2 is required for regeneration and homeostasis. Here, we identify a diverse population of approximately 32-nucleotide small RNAs that strongly resemble vertebrate and insect piRNAs and map to hundreds of thousands of loci in the S. mediterranea genome. The expression of these RNAs occurs predominantly in neoblasts and is not restricted to the germline. RNAi knockdown of either SMEDWI-2 or a newly identified PIWI protein, SMEDWI-3, impairs regeneration and homeostasis and decreases the levels of both piRNAs and neoblasts. Therefore, SMEDWI-2 and SMEDWI-3 are required for piRNA expression, regeneration, and neoblast function in S. mediterranea .