Rfoot: Transcriptome‐Scale Identification of RNA‐Protein Complexes from Ribosome Profiling Data

Ribosome profiling was developed to identify genome‐wide RNA fragments associated with translating ribosomes. However, no experimental procedure was developed to effectively purify ribosome‐RNA complexes. Actually, ribosome profiling is a transcriptomic RNase footprinting assay, which can identify both ribosomal and non‐ribosomal protein‐RNA complexes. Many sequencing reads represent functional RNA footprints associated with non‐ribosomal proteins. Here I present a computational pipeline named Rfoot to systematically identify genome‐wide non‐ribosomal RNA footprints, based on the highly localized read distribution feature. Analyses have revealed native functional protein‐RNA complexes in lncRNAs, 3′UTRs of mRNAs, and all types of small noncoding RNAs. This computational tool is useful for discovering novel noncoding functions of RNAs. © 2018 by John Wiley & Sons, Inc.