tRNA-like leader-trailer interaction promotes 3ʹ-end maturation of MALAT1

Abstract

Human metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a nuclear long noncoding RNA (lncRNA) that is highly overexpressed in many cancer tissues and plays important roles in tumor progression and metastasis. The MALAT1 primary transcript contains evolutionarily-conserved structural elements in its 3ʹ-terminal region: a triple helix forming element called element for nuclear expression (ENE) and a downstream tRNA-like structure called mascRNA. Instead of being polyadenylated, mature MALAT1 is generated by recognition and processing of the mascRNA by RNase P. Upon RNase P cleavage, a genomically-encoded A-rich tract at the new 3ʹ end of MALAT1 is liberated and forms a triple helical structure with the upstream ENE. Triplex formation is vital for stabilization of the mature transcript and for subsequent accumulation and oncogenic activity of MALAT1. Here, we demonstrate that efficient 3ʹ-end maturation of MALAT1 is dependent on an interaction between the A-rich tract and the mascRNA 3ʹ trailer. Using mutational analyses of an in vivo reporter accumulation, we show that an extended mascRNA acceptor stem and formation of a single bulged A 5ʹ to the RNase P cleavage site are required for efficient maturation of the nascent MALAT1 3′ end. Our results should benefit the development of therapeutic approaches to cancer through targeting MALAT1.