In vivo PAR-CLIP (viP-CLIP) of liver Tial1 unveils targets regulating cholesterol synthesis and secretion

System-wide cross-linking and immunoprecipitation (CLIP) approaches have unveiled regulatory mechanisms of RNA-binding proteins (RBPs) mainly in cultured cells due to limitations in the cross-linking efficiency of tissues. Here, we describe viP-CLIP (in vivo PAR-CLIP), a method capable of identifying RBP targets in mammalian tissues, thereby facilitating the functional analysis of RBP-regulatory networks in vivo. We applied viP-CLIP to mouse livers and identified Insig2 and ApoB as prominent TIAL1 target transcripts, indicating an important role of TIAL1 in cholesterol/triglyceride synthesis and secretion. The functional relevance of these targets was confirmed in Tial1 mice with loss and gain-of -function mutations revealing that mice with liver-specific Tial1 loss- and gain-of-function mutations impact on cholesterol synthesis, apoB secretion and plasma cholesterol levels. Our results demonstrate that viP-CLIP is capable of identifying physiologically relevant RBP targets by identifying a novel factor implicated in the negative feedback regulation of cholesterol biosynthesis.Overall design: viP-CLIP of Tial1 and poly(A) selected RNA-sequencing in mouse liver.