Self-recognition of an inducible host lncRNA by RIG-I feedback restricts innate immune response

In this study, we employed a combination of UV-RIP-seq, PacBio-seq and iCLIP-seq technologies to identify long non-coding RNA associated with cytoplasmic RIG-I protein in mouse macrophages cells. Overall design: Two UV-RIP were performed using anti-Flag antibody in RAW264.7 cells stably expressing Flag-tagged RIG-I with or without vesicular stomatitis virus (VSV) infection for 12 hr, then co-purified RNAs were analyzed using Illumina HiSeq4000 sequencing. One RIP was performed using anti-RIG-I antibody in RAW264.7 cells with VSV infection for 12 hr, then co-purified RNAs were sequenced using PacBio's SMRT long-read sequencing strategy. Total RNA from mouse peritoneal macrophages was analyzed using PacBio sequencing. iCLIP was performed using anti-RIG-I antibody in RAW264.7 cells upon VSV infection for 12 hr and then made Illumina HiSeq2500 SE50 Sequencing.