Fig. 4

CLIP-seq of T7-TRIM25 in HeLa cells reveals TRIM25’s RNA targets. a The distribution of TRIM25 CLIP-seq clusters in total RNA. b The ab initio-derived TRIM25-binding sequence preference. T is representative of U in the RNA. c GC content is significantly enriched in TRIM25 CLIP-seq clusters as compared to randomly selected transcripts or exons with a similar length distribution (transcripts detected in HeLa RNA-seq); P value 2.2 × 10^–16. d The distribution of TRIM25 CLIP-seq clusters in mRNAs. e The distribution of TRIM25 CLIP clusters across the protein coding genes reveals increased frequency in 5′- and 3′-UTRs. f, g RNA-immunoprecipitation (RIP) validates CLIP-seq data and PRY/SPRY as the RNA-interacting domain. HeLa cells were mock transfected, transfected with T7-TRIM25 or T7-TRIM25ΔRBD, and the extracts immunoprecipitated with anti-T7 antibody. f qRT-PCR results from RIP assay for selected protein coding and non-coding RNAs. The values are relative to those obtained from mock transfected cells, which were set to 1. The mean and standard deviations (SD) of three independent biological replicates are shown. g qRT-PCR results from RIP assay for selected miRs. The values are relative to those obtained from mock transfected cells, which were set to 1. The mean and SD of three independent biological replicates are shown