Functional characterization of protein SUMOylation in the miRNA transcription regulation during heat stress in Arabidopsis

MicroRNAs (miRNAs) play an essential role as non-coding-RNA-type epigenetic regulators in response to high-temperature stress in plants. There are crucial roles for global transcriptional regulation under SUMO (small ubiquitin-related MOdifier) stress response (SSR). However, the molecular mechanisms underlying its downstream regulation remain unclear. In this study, SUMO-specific chromatin immunoprecipitation sequencing analysis detected specific binding in the promoter region of miRNAs under high-temperature stress. A correlation analysis between this binding and miRNA profiling revealed that the location of SUMO on the chromosome was correlated with the expression pattern of miRNAs, particularly miR398a and miR824a. In contrast, knockout mutants of the SSR-dependent SUMO E3 ligase SAP AND MIZ 1 in Arabidopsis exhibited opposing trends in target gene expression for the SUMO-related miRNAs compared to the wild type. Multi-omics correlation analyses identified 34 SUMO-candidate proteins that might be involved in the regulation of miRNA response to high-temperature stress. Therefore, we propose a potential model whereby high-temperature exposure induces nuclear entry of SUMO molecules, modifying specific transcription factors that bind to miRNA gene promoters and potentially regulate miRNA expression. SUMO-substrate binding at miRNA promoters during high-temperature stress correlates with miRNA expression. High-temperature triggers nuclear SUMO entry, altering transcription factors to regulate miRNA gene promoters. SUMO could modify SPL10, SPL11, and TCP13 to regulate miRNAs during plant heat stress. The rapid regulation of stress-responsive gene expression mediated by microRNAs (miRNAs) plays a crucial role in responding to heat stress in the plant. Although there has been a substantial increase in the investigation of miRNA-target gene interactions under high-temperature stress conditions in crop plants, the involvement of protein modifications in miRNAs regulation remains unclear. In this study, we discovered that SUMO-modified proteins in Arabidopsis can bind to the promoter regions of miRNAs during high-temperature stress. Moreover, the impact of SUMO-specific modified proteins on the expression of miRNA was performed by a correlation analysis between small RNA and transcriptome data. Furthermore, by combining bioinformatics predictions and biochemical experiments, we have predicted 34 transcriptional factors as binding to the promoters of SUMO-related miRNAs and confirmed two transcription factors to be substrates for SUMOylation.