CLICK-seq of DL1 cells following Brat RNAi

This study identified novel targets of the RNA-binding protein Brat. Unlike previously published transcriptome-wide analyses, endogenous Brat protein and mRNA were efficiently depleted, via RNA interference, in a homogenous cell population. Two RNAi conditions, in combination with replicates and rigorous analysis, identified genes significantly increased following depletion of Brat. RNAi of Brat was compared to cells treated with non-targeting control dsRNA. Click-Seq was performed on poly(A) selected RNA. Aspects of these genes, such as motifs enriched and overlap with published datasets, further provided insight into regulation of mRNA stability by Brat. Finally, follow-up and complementary experiments further validated these targets.