The METHYLTRANSFERASE B–SERRATE interaction mediates the reciprocal regulation of microRNA biogenesis and RNA m6A modification

• Published in: Journal of integrative plant biology 2024-12, Vol.66 (12), p.2613-2631
• Main Authors: Bai, Haiyan, Dai, Yanghuan, Fan, Panting, Zhou, Yiming, Wang, Xiangying, Chen, Jingjing, Jiao, Yuzhe, Du, Chang, Huang, Zhuoxi, Xie, Yuting, Guo, Xiaoyu, Lang, Xiaoqiang, Ling, Yongqing, Deng, Yizhen, Liu, Qi, He, Shengbo, Zhang, Zhonghui
• Format: Article
• Language: English
• Subjects: Binding; biogenesis; Biosynthesis; Cell and Developmental Biology; Chromatin; Epigenetics; Eukaryotes; eukaryotic cells; Fluorescence recovery after photobleaching; Liquid phases; liquid–liquid phase separation; methyltransferases; Microprocessors; microRNA; microRNA biogenesis; MicroRNAs; miRNA; MTB; mutants; N6-methyladenosine; Organelles; Phase separation; Photobleaching; plant biology; Regulation; Regulatory mechanisms (biology); Ribonucleic acid; RNA; RNA m6A modification; RNA modification; RNA-mediated interference; separation; solubility; Transcriptomes
• ISSN: 1672-9072; 1744-7909; 1744-7909
• DOI: 10.1111/jipb.13770

ABSTRACT In eukaryotes, RNA N6‐methyladenosine (m6A) modification and microRNA (miRNA)‐mediated RNA silencing represent two critical epigenetic regulatory mechanisms. The m6A methyltransferase complex (MTC) and the microprocessor complex both undergo liquid–liquid phase separation to form nuclear membraneless organelles. Although m6A methyltransferase has been shown to positively regulate miRNA biogenesis, a mechanism of reciprocal regulation between the MTC and the microprocessor complex has remained elusive. Here, we demonstrate that the MTC and the microprocessor complex associate with each other through the METHYLTRANSFERASE B (MTB)–SERRATE (SE) interacting module. Knockdown of MTB impaired miRNA biogenesis by diminishing microprocessor complex binding to primary miRNAs (pri‐miRNAs) and their respective MIRNA loci. Additionally, loss of SE function led to disruptions in transcriptome‐wide m6A modification. Further biochemical assays and fluorescence recovery after photobleaching (FRAP) assay indicated that SE enhances the liquid–liquid phase separation and solubility of the MTC. Moreover, the MTC exhibited enhanced retention on chromatin and diminished binding to its RNA substrates in the se mutant background. Collectively, our results reveal the substantial regulatory interplay between RNA m6A modification and miRNA biogenesis. In Arabidopsis, METHYLTRANSFERASE B (MTB)–SERRATE (SE) interaction links RNA m6A methylase complex and microprocessor, affecting microRNA production and m6A modification. Knockdown of MTB impairs microRNA biogenesis and loss of SE function disrupts transcriptome‐wide m6A modification. SE enhances the liquid‐liquid phase separation and solubility of the m6A methylase complex.