Structural basis of MALAT1 RNA maturation and mascRNA biogenesis

MALAT1 lncRNA plays key roles in regulating transcription, splicing, and tumorigenesis. Its maturation and stabilization require precise processing by RNase P, which simultaneously initiates the biogenesis of a 3' cytoplasmic mascRNA. mascRNA was proposed to fold into a tRNA-like secondary structure, but lacks eight conserved linking residues required by the canonical tRNA fold. Here, we report crystal structures of human mascRNA before and after processing, which reveal an ultracompact, quasi-tRNA-like structure. Despite lacking all linker residues, mascRNA faithfully recreates the characteristic “elbow” feature of tRNAs to recruit RNase P and ELAC2 for processing, which exhibit distinct substrate specificities. Rotation and repositioning of the D-stem and anticodon regions preclude mascRNA from aminoacylation, avoiding interference with translation. Therefore, a class of metazoan lncRNAs employ a previously unrecognized, unusually streamlined quasi-tRNA architecture to recruit select tRNA-processing enzymes while excluding others, to drive bespoke RNA biogenesis, processing, and maturation. Overall design: We performed sequencing to examine the processing of WT and mutant pre-mascRNAs in Flp-In 293 cells expressed from transfected plasmids