Regulation of a maize HD-ZIP IV transcription factor by a non-conventional RDR2-dependent small RNA

Abstract

Small non-coding RNAs are versatile riboregulators that control gene expression at the transcriptional or post-transcriptional level, governing many facets of plant development. Here we present evidence for the existence of a 24 nt small RNA (named small1) that is complementary to the 3′ UTR of OCL1 (Outer Cell Layer1), the founding member of the maize HD-ZIP IV gene family encoding plant-specific transcription factors that are mainly involved in epidermis differentiation and specialization. The biogenesis of small1 depends on DICER-like 3 (DCL3), RNA-dependent RNA polymerase 2 (RDR2) and RNA polymerase IV, components that are usually required for RNA-dependent DNA-methylation. Unexpectedly, GFP sensor experiments in transient and stable transformation systems revealed that small1 may regulate its target at the post-transcriptional level, mainly through translational repression. This translational repression is attenuated in an rdr2 mutant background in which small1 does not accumulate. Our experiments further showed the possible involvement of a secondary stem-loop structure present in the 3′ UTR of OCL1 for efficient target repression, suggesting the existence of several regulatory mechanisms affecting OCL1 mRNA stability and translation. Significance StatementThis work addresses the question of the regulation of the plant specific HD-ZIP IV transcription factors by an atypical non coding small RNA. Although the biogenesis of this small RNA depends on components of the transcriptional gene silencing machinery such as DCL3 RDR2 and Pol IV, our results strongly suggest that it regulates its target at the post-transcriptional level, mainly through translational repression.