Histone methylation reader MRG2 interacts with exon junction complex component eIF4A3 to regulate alternative splicing in Arabidopsis (PRJCA041145)

Alternative splicing (AS) is an important regulatory mechanism for fine-tuning gene transcription in eukaryotes. H3K36me3 is known to function in AS regulation, but the underlying mechanisms remain largely obscure. In this study, we showed that the Arabidopsis thaliana H3K36me3 reader protein MORF-related gene 2 (MRG2) directly interacts with eIF4A3, a component of the exon junction complex within the spliceosome. The eif4a3 mutant displayed a late flowering phenotype similar to that of the mrg1 mrg2 double mutant under long-day but not short-day photoperiod conditions. Transcriptome analysis showed that deleting either eIF4A3 or MRG1/MRG2 caused similar changes in gene transcription and AS events, which are involved in diverse physiological processes, including circadian rhythm regulation and responses to environmental stimuli. Both eIF4A3 and MRG1/MRG2 are required for the AS of key circadian clock genes and the maintenance of an appropriate circadian rhythm. Chromatin immunoprecipitation analysis showed that eIF4A3 and MRG2 directly target and enhance each other's binding to the key circadian clock genes PRR7 and PRR9. RNA immunoprecipitation sequencing data revealed that MRG1/2 facilitate the specific binding of eIF4A3 to the key circadian clock genes PRR7 and PRR9 RNAs. Collectively, our findings establish a direct link between histone modification and the splicing machinery, revealing that the reader protein MRG2 recognizes histone methylation signals and recruits eIF4A3 to regulate co-transcriptional AS events in plants.