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.