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

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• Ribosome profiling identifies genome-wide RNA fragments linked to translating ribosomes.
• Existing methods lack effective purification for ribosome-RNA complexes.
• Ribosome profiling can detect both ribosomal and non-ribosomal protein-RNA complexes.

Purpose of the Study:

• To develop a computational pipeline for systematic identification of genome-wide non-ribosomal RNA footprints.
• To analyze functional protein-RNA complexes beyond translating ribosomes.

Main Methods:

• Development of a computational pipeline named Rfoot.
• Utilizing the highly localized read distribution feature of sequencing reads.
• Application to analyze RNA fragments associated with both ribosomal and non-ribosomal proteins.

Main Results:

• Identification of genome-wide non-ribosomal RNA footprints.
• Discovery of native functional protein-RNA complexes in lncRNAs, 3'UTRs of mRNAs, and small noncoding RNAs.
• Demonstration of Rfoot's utility in uncovering novel RNA functions.

Conclusions:

• Rfoot effectively identifies non-ribosomal RNA footprints.
• The pipeline reveals diverse functional protein-RNA interactions.
• This tool advances the discovery of novel noncoding RNA functions.