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mRNAs with a complex: The long‐term consequences of a nuclear upbringing

As pre‐mRNAs mature into mRNAs in the nucleus, they are decorated with proteins that impact their subsequent fate in the cytoplasm. Pre‐mRNA splicing stably deposits a set of proteins (the exon junction complex, EJC) 20‐24 nucleotides upstream of exon junctions. EJCs thus assembled preserve the splicing history of an mRNA and also serve as binding platforms for other proteins mediating downstream events such as mRNA surveillance, translation and mRNA localization. Work in recent years has elucidated the protein composition of the EJC and the molecular interactions required for EJC assembly as well as its molecular architecture at the atomic level. Nonetheless, many fundamental questions regarding the EJC remain, such as: Are EJCs deposited after splicing on all exon‐exon junctions of an mRNA? Are EJCs always deposited at the same position in relation to every exon‐exon junction? Are EJCs exclusive to exon‐exon junctions, or do they bind to other sites on mRNAs or unspliced RNAs? To address these questions, we purified EJCs from cell lines stably expressing FLAG‐tagged EJC proteins at near endogenous levels. EJCs thus purified exhibit a defined RNA footprint that was used to generate short cDNA libraries for Deep Sequencing. These genome‐wide deposition profiles will enhance and broaden our understanding of the EJC's contribution to post‐transcriptional gene regulation.