Sequential onset and concurrent expression of miR-9 genomic loci in single cells contributes to the temporal increase of mature miR-9 in zebrafish neurogenesis

MicroRNAs (miRs) have important quantitative roles in tuning dynamical gene expression. Hes/Her transcription factor dynamics are sensitive to the increasing amount of miR-9 in the cell, transitioning from noisy high-level expression to oscillatory expression and then to downregulation. However, the mechanism by which miR-9 is quantitatively controlled is not known. In vertebrates, several distinct genomic loci produce the same mature miR-9, but the functional significance of multiple primary transcripts remains unknown. Here, we show that the amount of mature miR-9 increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize the spatiotemporal profile of 7 distinct pri-mir-9s and show that they are sequentially expressed during hindbrain neurogenesis. Quantitative analysis of expression at the single-cell level, shows that expression of late-onset pri-mir-9-1 is added on, rather than replacing the expression of early onset pri-mir-9-4 and 9-5. Mutating the late-onset pri-mir-9-1 with CRISPR/Cas9 prevents the developmental increase of mature miR-9 and reduces late neuronal differentiation. Finally, we use mathematical modelling to explore possible benefits of a stepwise increase of miR-9 over a linear increase. We find that an adaptive network containing Her6 can be insensitive to a linear increase in miR-9 and show that such adaptation can be overcome by step-wise increases of miR-9. In conclusion, our work suggests that a sharp stepwise increase of mature miR-9 is contributed by sequential temporal activation of distinct loci. This may be a strategy to overcome adaptation and facilitate a transition to a new state of Her6 dynamics or level.