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

Zhe Ji

doi:10.1002/cpmb.66

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

Zhe Ji^*

^*Corresponding author for this work

Pharmacology

Research output: Contribution to journal › Article › peer-review

8 Scopus citations

Abstract

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.

Original language	English (US)
Article number	e66
Journal	Current Protocols in Molecular Biology
Volume	124
Issue number	1
DOIs	https://doi.org/10.1002/cpmb.66
State	Published - Oct 2018

Funding

I thank scientists who tried Rfoot and provided feedback to improve the software. The work was supported by grants to Z. J. from the National Institutes of Health (CA 207865) and from Northwestern University (the Searle Leadership Fund in the Life Sciences).

Keywords

RNase footprinting
lncRNA
non-ribosomal protein-RNA complex
ribosome profiling
small noncoding RNA

ASJC Scopus subject areas

Molecular Biology

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10.1002/cpmb.66

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abstract = "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.",

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

Abstract

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Keywords

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