Alternative splicing (AS) is an important regulatory mechanism for fine-tuning gene transcription in eukaryotes. H3K36me3 affects AS, but the underlying mechanisms remain 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 displays 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 causes similar changes in gene transcription and AS, which are involved in diverse 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. RNA immunoprecipitation sequencing (RIP-seq) showed that MRG1/MRG2 promote eIF4A3 binding to the transcripts of a set of genes, including the key circadian clock genes PSEUDO-RESPONSE REGULATOR 7 (PRR7) and PRR9. Moreover, eIF4A3 and MRG2 directly target and enhance each other's binding to PRR7 and PRR9 chromatin. Collectively, our findings reveal that the reader protein MRG2 recognizes histone methylation signals and recruits eIF4A3 to regulate co-transcriptional AS events, establishing a direct link between histone modification and the splicing machinery in plants.
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