Circular RNAs derived from MIR156D promote rice heading by repressing transcription elongation of pri-miR156d through R-loop formation

In angiosperms, microRNA156 (miR156) acts as an intrinsic, endogenous developmental timer for the age-dependent transition from the juvenile to the adult phase^1,2,3. However, the mechanisms modulating the age-dependent expression pattern of miR156 are still poorly understood⁴. In this Article, we report that circular RNAs (ciMIR156Ds) derived from pri-miR156d negatively regulate miR156 levels in an aging-dependent manner in rice. The ciMIR156D levels increase as plants age, which is inversely correlated with the changes of pri-miR156d and miR156 abundance. Consistent with this observation, ciMIR156Ds deficiency caused by a spontaneous mutation increases pri-miR156d and miR156 levels, resulting in a delayed heading phenotype, whereas ciMIR156Ds overexpression has opposite effects, demonstrating that ciMIR156Ds are negative regulators of miR156. We further show that ciMIR156Ds form R-loops with MIR156D at the region where they derive in an aging-dependent manner, which reduces the occupancy of DNA-dependent RNA polymerase II at that location and hence impedes pri-miR156d elongation. These findings reveal a mechanism for regulating heading date by refining the aging-dependent expression of miR156.