UV-crosslinking immunoprecipitation sequencing of RNAs bound to duck RIG-I in immortalized duck embryonic fibroblasts

Using UV-CLIP-Seq, we mapped RIG-I-RNA interactions in three independent duck embryonic fibroblast (DEF) clones expressing 3xFLAG-RIG-I. Cells were stimulated with 5-ppp-dsRNA, UV-crosslinked to stabilize protein-RNA complexes, and lysed for anti-FLAG immunoprecipitation. After reversing crosslinks and purifying RNA, we checked samples by Qubit and Bioanalyzer, prepared libraries with Novogene, and found no direct binding of lnc455 (or other candidate lncRNAs) to activated RIG-I, indicating lnc455 acts indirectly to enhance type I interferon signaling.