Debranching enzyme DBR1-mediated lariat RNA turnover requires ALBA proteins in Arabidopsis

Lariat RNAs, generated as by-products of RNA splicing from excised introns, must be removed. RNA debranching enzyme (DBR1) is the core factor responsible for lariat RNA removal. However, the mechanism by which DBR1 debranches lariat RNAs remains unclear. Here, we demonstrate that six ALBA (Acetylation Lowers Binding Affinity) proteins interact with DBR1 to enhance its debranching activity and facilitate DBR1's accessibility to lariat RNAs, thereby promoting lariat RNA turnover. Similar to dbr1, alba mutants exhibit pleiotropic developmental defects and accumulate lariat RNAs. ALBAs bind to lariat RNAs via their C-terminal RGG/RG-rich repeats and assist DBR1 in binding to these RNAs. The N-terminal ALBA domain mediates the interaction with DBR1 and enhances its enzymatic activity. Cold stress induces lariat RNA accumulation by attenuating the ALBA–DBR1 interaction, which in turn reduces the induction of cold-responsive genes by impairing their transcription. Together, these findings uncover that lariat RNA turnover requires ALBA proteins. Overall design: Lariat RNA-seq for four genotypes plants under normal condition or cold treatment was performed with 3 biological replicates each. Lariat RNA-seq for transgenic plants and albah was performed with 3 biological replicates each. RIP-seq for GFP and ALBA5 in Col-0 and dbr1-2 was performed with 2 biological replicates each. RIP-seq for DBR1(H85A) in Col-0 and alba456 was performed with 2 biological replicates each.