Protocol for identification of intronic lariat RNAs by RNA deep sequencing in Arabidopsis thaliana

Lariat RNAs formed from excised introns during RNA splicing typically undergo DBR1-mediated debranching and degradation; however, many lariat RNAs accumulate stably in various organisms. Here, we present a protocol for constructing RNA sequencing libraries and a bioinformatic pipeline to identify intronic lariat RNAs in Arabidopsis thaliana . We describe steps for extracting and enriching RNA, library preparation, and capturing reads flanking branchpoint-to-5′ splice site junctions through sequencing. We then detail procedures to identify lariat RNAs derived from excised introns using computational screening. For details on the original application and validation of this protocol, please refer to Ge et al. 1