tRNA-like leader-trailer interaction promotes 3′-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 3′-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. A genomically encoded A-rich tract at the new 3′ end of MALAT1, which is generated upon RNase P cleavage, 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 3′-end maturation of MALAT1 is dependent on an interaction between the A-rich tract and the mascRNA 3′ trailer. Using mutational analyses of cell-based reporter accumulation, we show that an extended mascRNA acceptor stem and formation of a single bulged A 5′ 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.