Genome-wide RNA structure changes during human neurogenesis modulate gene regulatory networks
RNAs structures play central roles in various cellular processes, and can be remodeled upon binding to cellular factors such as RNA binding proteins (RBP). However, how widespread this remodeling is and whether structural changes can serve as additional regulatory steps for other regulators remains under-explored. Here, we assayed RNA structural dynamics, gene expression, translation and decay during different stages of human neuronal differentiation to understand the impact of RNA structures in stem cell regulation. RBP binding resulted in wide-spread RNA structure changes during early neuronal differentiation.  Structure changes act as a common mechanism for RBPs to modulate the binding of additional RBPs and miRNAs to coordinate gene expression temporally.  In particular, we showed that PUM2 binding on LIN28A resulted in RNA structure changes that enabled miR-30 binding, leading to downregulation of LIN28A. Compensatory mutagenesis experiments that lock specific structural states confirmed the importance of PUM2-induced structure changes in miR-30 regulation. This systematic study broadens our understanding of RNA structural dynamics during human neuronal differentiation and illustrates the wide-spread and complex role of RBPs in regulating RNA structures for gene regulation during human development. Overall design: High throughput RNA structure probing experiments in vivo using icSHAPE in hESCs (Day 0, D0), neuronal precursor cells (Day 7, D7), early neurons (Day 8, D8) and neurons (Day 14, D14).