An antisense intragenic lncRNA SEAIRa mediates transcriptional and epigenetic repression of in .

SERRATE (SE) is a core protein for microRNA (miRNA) biogenesis as well as for mRNA alternative splicing. Investigating the regulatory mechanism of expression is hence critical to understanding its detailed function in diverse biological processes. However, little about the control of expression has been clarified, especially through long noncoding RNA (lncRNA). Here, we identified an antisense intragenic lncRNA transcribed from the 3' end of , named SEAIRa. SEAIRa repressed expression, which in turn led to serrated leaves. SEAIRa recruited plant U-box proteins PUB25/26 with unreported RNA binding ability and a ubiquitin-like protein related to ubiquitin 1 (RUB1) for H2A monoubiquitination (H2Aub) at exon 11 of . In addition, PUB25/26 helped cleave SEAIRa and release the 5' domain fragment, which recruited the PRC2 complex for H3 lysine 27 trimethylation (H3K27me3) deposition at the first exon of . The distinct modifications of H2Aub and H3K27me3 at different sites of the locus cooperatively suppressed expression. Collectively, our results uncover an epigenetic mechanism mediated by the lncRNA SEAIRa that modulates expression, which is indispensable for plant growth and development.