Mapping snoRNA-target RNA interactions in an RNA binding protein-dependent manner with chimeric eCLIP [chimeric eCLIP]

To indentify the targets of snoRNAs, we adapted an enhanced chimeric eCLIP approach,utilizing both established core proteins and lesser-known snoRNA-associated RBPs as bait. . Overall design: We perform chimeirc eCLIP using C/D box snoRNA binding proteins (FBL, NOP56, NO58) as bait in both mouse ESCs and human cell lines and H/ACA snoRNA binding proteins (DKC1, GAR1) as bait in human cell lines; we also performed chimeric eCLIP with the accessory snoRNA binding proteins (LARP7, NOLC1, WDR43, UPT18, ZC3H8, SMNDC1) to capture snoRNA interactions.