SCRIBE · Stem cell riboregulation: a new layer to control self-renewal, differentiation and metabolism

Although multiple regulatory layers have been reported to control stem cell differentiation, including epigenetics, cell signaling and metabolism, we still lack sufficient knowledge on how differentiation processes are connected and coordinated. The Hentze laboratory recently discovered that RNA modulates (riboregulates) the activity of the glycolytic enzyme Enolase 1 (ENO1) and that this interaction is essential for in vitro murine embryonic stem cell differentiation. Additionally, unpublished data from the laboratory show that the glycolytic enzyme pyruvate kinase (PKM) is also riboregulated. However, the role of riboregulation during primary stem cell differentiation remains elusive. Previously, RNA-bound proteomes have either been identified in cultured cells or ex vivo in whole organs. I aim to investigate enzyme-RNA interactions in primary stem cells and differentiated progeny, using the hematopoietic system as a model. First, I will analyze the RNA-binding activity of previously in cellulo profiled enzymes ENO1 and PKM in vivo and ex vivo during hematopoietic stem cell (HSC) differentiation by RNA-proximity ligation assays, profiling of stem cell activity and transcriptome analysis (aim 1). Secondly, I will analyze, identify and comparatively quantify global RNA-protein interactions in HSCs, progenitors and mature blood cells by developing a method to profile in vivo RNA-protein interactions (aim 2). In an interdisciplinary approach, I will pair fluorescence-activated cell sorting with state-of-the-art RNA-protein cross-linking approaches and ultra-low input proteomics analysis. The generated data will help, for the first time, to understand at the analytical and functional level whether and to what degree riboregulation of enzymes represents a regulatory paradigm operational in mammalian cells, with a focus on hematopoietic stem cell differentiation.