Why RNA binding proteins should be studied in the context of their subcellular location; the case of Myotonic Dystrophy type 2 associated gene CNBP/ZNF9

CNBP is conserved in eukaryotes and essential for embryonic development. A CCTG repeat expansion in intron#1 of CNBP is linked to Myotonic Dystrophy Type 2. To-date, the leading model of pathogenesis suggests gain of toxicity by sequestration of essential factors to the expanded repeat. However, several reports support a loss of function mechanism. Recently we showed that CNBP is a cytoplasmic RNA binding protein targeting mRNA elements that fold into G-quadruplex structures in vitro or when expressed in bacteria yet remain unfolded in eukaryotic cells. We revealed that CNBP binding facilitates translation of its mRNA targets, and thus proposed that CNBP promotes translation by reducing inhibitory RNA structures. Our more recent work revealed that proteins whose translation is promoted by CNBP are 6-fold enriched with mitochondrial inner membrane proteins(p-value<10^-30), and that CNBP knockout results in accelerated acidification of growth media. Seahorse measurements confirmed CNBP knockout cells have an increased glycolysis to oxidative phosphorylation rates ratio. Multiple evidence suggest that nuclear-encoded mitochondrial proteins are translated in proximity to mitochondria. Therefore, to test whether CNBP associates with its mRNA targets on the mitochondrial surface, we are currently refining our recently developed method, Proximity-CLIP, which will enable capturing CNBP targets at subcellular resolution.