Hyponastic Leaves 1 Interacts with RNA Pol II to Ensure Proper Transcription of MicroRNA Genes

Abstract

HYL1 (DRB1) is a double-stranded RNA binding protein involved in miRNA processing in plants. It is a core component of the Microprocessor complex and enhances the efficiency and precision of miRNA processing by the DCL1 protein. In this work, we report a novel function of the HYL1 protein in the transcription of MIR genes. HYL1 colocalizes with RNA Polymerase II and affects its distribution along MIR genes. Moreover, proteomic experiments revealed that the HYL1 protein interacts with many transcription factors. Finally, we show that the action of HYL1 is not limited to MIR genes and impacts the expression of many other genes, a majority of which are involved in the plastid organization. These discoveries indicate HYL1 as an additional player in gene regulation at the transcriptional level, independent of its role in miRNA biogenesis.

The HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE15–HISTONE DEACETYLASE9 complex associates with HYPONASTIC LEAVES 1 to modulate microRNA expression in response to abscisic acid signaling

“…2, E to H ). These results resemble previous results showing that HYL1 interacts with TOPLESS (TPL) and TOPLESS-RELATED (TPR1 and TPR2), Lish-WD40 proteins with functions in chromatin remodeling ( Bielewicz et al 2023 ). This suggests that HYL1 is prone to interact with regulatory factors, likely at the chromatin level.…”

“…Later, further research using HYL1 loss of function mutants revealed many biological aspects of this protein, positioning it as one of the major miRNA biogenesis components in plants. Recently, a few studies also hint at the possibility that HYL1 acts outside the miRNA biogenesis regulating miRNA-mediated translation inhibition and MIRNA transcription ( Yang et al 2021 ; Bielewicz et al 2023 ). Interaction assays revealed that HYL1 associates with TPL, TPR1, TPR2, and TPR4, which are Lish-WD40 proteins known to repress transcription ( Bielewicz et al 2023 ), indicating a tight link between the miRNA processing machinery and transcription.…”

“…Recently, a few studies also hint at the possibility that HYL1 acts outside the miRNA biogenesis regulating miRNA-mediated translation inhibition and MIRNA transcription ( Yang et al 2021 ; Bielewicz et al 2023 ). Interaction assays revealed that HYL1 associates with TPL, TPR1, TPR2, and TPR4, which are Lish-WD40 proteins known to repress transcription ( Bielewicz et al 2023 ), indicating a tight link between the miRNA processing machinery and transcription. Still, whether HYL1 has a direct effect on transcription or promotes the recruitment of transcriptional regulators remains unclear.…”

“…Whether the recruitment of HYL1 to the nascent pri-miRNAs depends on the formation of the processing complex or is the consequence of a direct recognition of the naked stem–loop transcript is unknown. In either case, the HYL1–pri-miRNA interaction causes HYL1 to interact with the transcriptional machinery, potentially regulating gene expression at the level of chromatin ( Bielewicz et al 2023 ). In turn, the ability of HYL1 to interact with the pri-miRNA dsRNA stem and mature miRNA duplex is a dynamic light-dependent turnover mechanism that constitutes a central hub to fine-tune miRNA activity in plants ( Manavella et al 2012 ; Cho et al 2014 ; Yang et al 2014 ; Achkar et al 2018 ; Choi et al 2020 ; Tomassi et al 2020 ).…”