mRNA adenosine methylase (MTA) deposits m
6A on pri-miRNAs to modulate miRNA biogenesis in
Arabidopsis thaliana.
Proc Natl Acad Sci U S A 2020;
117:21785-21795. [PMID:
32817553 PMCID:
PMC7474595 DOI:
10.1073/pnas.2003733117]
[Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Recently N6-methyladenosine (m6A) methylation has emerged as a biological process with significant impact on cellular functions. However, almost all the research regarding m6A methylation has been based on mRNAs. In our research, we focus on how m6A methylation affects microRNA (miRNA) biogenesis in Arabidopsis. In brief, we show that m6A methylation is necessary to maintain proper levels of mature miRNAs as well as their precursors. m6A mark affects pri-miRNA secondary structures and affects the recruitment of the Microprocessor to pri-miRNAs. We also demonstrate the interactions of MTA (m6A writer) with other proteins involved in miRNA biogenesis, namely RNA Polymerase II and TOUGH. Our study provides evidence of the role played by m6A in plant miRNA biogenesis.
In Arabidopsis thaliana, the METTL3 homolog, mRNA adenosine methylase (MTA) introduces N6-methyladenosine (m6A) into various coding and noncoding RNAs of the plant transcriptome. Here, we show that an MTA-deficient mutant (mta) has decreased levels of microRNAs (miRNAs) but accumulates primary miRNA transcripts (pri-miRNAs). Moreover, pri-miRNAs are methylated by MTA, and RNA structure probing analysis reveals a decrease in secondary structure within stem–loop regions of these transcripts in mta mutant plants. We demonstrate interaction between MTA and both RNA Polymerase II and TOUGH (TGH), a plant protein needed for early steps of miRNA biogenesis. Both MTA and TGH are necessary for efficient colocalization of the Microprocessor components Dicer-like 1 (DCL1) and Hyponastic Leaves 1 (HYL1) with RNA Polymerase II. We propose that secondary structure of miRNA precursors induced by their MTA-dependent m6A methylation status, together with direct interactions between MTA and TGH, influence the recruitment of Microprocessor to plant pri-miRNAs. Therefore, the lack of MTA in mta mutant plants disturbs pri-miRNA processing and leads to the decrease in miRNA accumulation. Furthermore, our findings reveal that reduced miR393b levels likely contributes to the impaired auxin response phenotypes of mta mutant plants.
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