SMaRT lncRNA controls translation of a G-quadruplex containing mRNA antagonizing the DHX36 helicase

Guanine-quadruplexes (G4) present in RNA and DNA exert a number of different functions in the nucleus and in the cytoplasm. However, the molecular mechanisms of G4-mediated regulation are still poorly understood. We describe a regulatory circuitry operating in the early phases of muscle differentiation in which a long non coding RNA (SMaRT) base pairs with a G4-containing mRNA (Mlx-g) and represses its translation in an antagonistic way with the RNA helicase DHX36. MLX-g is required to allow the nuclear translocation of the MLX-a and b dimerization partners and to control proper myogenesis. We show that by controlling MLX-g, lnc-SMaRT is able to regulate the overall quantity of nuclear MLX proteins and their transcriptional output. Therefore, the circuitry composed by lnc-SMaRT, Mlx-g and Dhx36 not only plays an important role in the control of myogenesis but unravels a molecular mechanism where G4 structures and G4 unwinding activities are controlled in vivo. High-throughput sequencing of total RNA from C2C12 cells treated with si-Scr and si-SMaRT collected after two days from switch to differentiation medium ; High-throughput sequencing of total RNA from lnc-SMaRT pull-down experiments performed using specific and aspecific (LacZ) biotynilated antisense probes.