The Integrator complex regulates differential snRNA processing and fate of adult stem cells in the highly regenerative planarian Schmidtea mediterranea

摘要

In multicellular organisms, cell type diversity and fate depend on specific sets of transcript isoforms generated by post-transcriptional RNA processing. Here, we used Schmidtea mediterranea , a flatworm with extraordinary regenerative abilities and a large pool of adult stem cells, as an in vivo model to study the role of Uridyl-rich small nuclear RNAs (UsnRNAs), which participate in multiple RNA processing reactions including splicing, in stem cell regulation. We characterized the planarian UsnRNA repertoire, identified stem cell-enriched variants and obtained strong evidence for an increased rate of UsnRNA 3’-processing in stem cells compared to their differentiated counterparts. Consistently, components of the Integrator complex showed stem cell-enriched expression and their depletion by RNAi disrupted UsnRNA processing resulting in global changes of splicing patterns and reduced processing of histone mRNAs. Interestingly, loss of Integrator complex function disrupted both stem cell maintenance and regeneration of tissues. Our data show that the function of the Integrator complex in UsnRNA 3’-processing is conserved in planarians and essential for maintaining their stem cell pool. We propose that cell type-specific modulation of UsnRNA composition and maturation contributes to in vivo cell fate choices, such as stem cell self-renewal in planarians. Author summary Stem cells not only give rise to all specialized cell types of the body through differentiation but also to new stem cells through the process of self-renewal. Modifications of messenger RNAs (mRNAs) following their transcription play an important role in a stem cell’s decision between self-renewal and differentiation. However, since these cells are rare and difficult to access in mammals, the underlying mechanisms have mostly been studied in cultured cells. Here, we employ the planarian flatworm Schmidtea mediterranea that maintains a large pool of highly potent stem cells throughout life as an in vivo model to analyze the function of UsnRNAs, important regulators of multiple mRNA processing steps, in stem cell regulation. We show that stem cells express more UsnRNA sequence variants compared to differentiated cells. Moreover, the activity of the Integrator complex, which mediates UsnRNA maturation, is increased in stem cells. Depletion of Integrator complex components disrupts their global splicing pattern and affects the processing of histone mRNAs resulting in the loss of stem cell self-renewal and, consequently, in defects of tissue homeostasis and regeneration. Thus, we propose that planarian stem cell self-renewal in vivo depends on differential variant expression and efficient processing of UsnRNAs.