Abscisic acid-regulated microRNA biogenesis through HYPONASTIC LEAVES1

Received May 7, 2023. Accepted May 10, 2023. Advance access publication May 16, 2023 © The Author(s) 2023. Published by Oxford University Press on behalf of American Society of Plant Biologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Open Access In B ri ef


In Brief
The central dogma of molecular biology describes the genetic information flow from DNA to RNA to protein (Crick 1958). Since then, many noncoding RNAs and other exceptions to the dogma have been discovered and found to play critical roles in diverse biological processes without expressing proteins (Cech and Steitz 2014). In new research conducted by Junghoon Park and colleagues (Park et al. 2023), the authors studied the biogenesis of microRNAs (miRNAs), a type of noncoding RNAs that post-transcriptionally regulates gene expression. They found that HYPONASTIC LEAVES1 (HYL1), a core protein of the miRNA biogenesis machinery, is essential for regulating miRNA expression in response to abscisic acid (ABA) signaling in Arabidopsis.
Using a luciferase reporter system to monitor miRNA production, the authors performed a forward genetic screen to isolate Arabidopsis mutants with impaired miRNA biogenesis and activity. One of the mutants is mapped to HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE 15 (HOS15). A hos15 mutant was previously identified in a screen for mutations with altered expression of stress-induced genes (Zhu et al. 2008). The new hos15 mutant allele isolated by Park et al. displayed several morphological phenotypes, such as delayed flowering and shortened stems. Complementation confirmed that hos15 was the causal mutation for these phenotypes. To investigate the role of HOS15 in the miRNA pathway, the authors tested protein-protein interactions between HOS15 and several miRNA biogenesis factors. Only HYL1 showed an interaction with HOS15, indicating HOS15 regulates miRNA processing through HYL1.
HOS15 encodes a nuclear protein with dual functions as an E3-ligase substrate receptor and a transcriptional co-repressor protein. The authors suggest that the E3-ligase substrate receptor function of HOS15 is not involved in the miRNA pathway because HYL1 degradation is independent of E3-mediated ubiquitination. Therefore, they hypothesized that HOS15 works as a transcriptional co-repressor in the miRNA pathway. They began to test this hypothesis by assessing the interaction between HYL1 and known partners of HOS15, using yeast-2-hybrid and co-immunoprecipitation assays. They discovered that HYL1 interacts with 2 histone deacetylases: HDA9 and HDA15. HOS15-HDA9 is a well-defined stress-responsive complex (Park et al. 2018). Furthermore, HYL1 influences epigenetic marks, as evidenced by the increased levels of histone acetylation observed in hyl1, hda9, and hos15 mutants.
Chromatin immunoprecipitation sequencing (ChIP-Seq) analysis revealed that both HOS15 and HDA9 bind to many MIRNA loci. The bound loci did not have any obvious sequence motifs in common. The authors also conducted ChIP-qPCR assays to test the recruitment of HOS15 to MIRNA loci and observed that such associations were lost in the hyl1 mutant, suggesting HYL1 plays a crucial role in this process. Interestingly, ABA treatment facilitates this recruitment, which ultimately triggers histone deacetylation. miRNAs. Surprisingly, no noticeable change was found in pri-miRNA levels in either mutant. To investigate this inconsistency between pri-miRNA level and mature miRNA accumulation, a RNA polymerase II (Pol II) occupancy assay was performed. Significant enrichment of Pol II at MIRNA loci in both control and ABA conditions was observed in hos15 and hda9 mutants, indicating an enhancement of pri-miRNA transcription.
This study proposes an intriguing model ( Fig.) by which plants regulate ABA-mediated miRNA production. The HOS15-HDA9 complex uses HYL1 and pri-miRNA as the scaffold to target the upstream of MIRNA loci, remove histone acetylation marks, and repress the miRNA processing. Considering the known functions of HYL1 as a regulator of transcription and stability, this work shows that HOS15-HDA9 regulates some MIRNA genes at both transcriptional and processing levels upon interaction with HYL1.