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

Current Protocols in Molecular Biology
Zhe Ji

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. © 2018 by John Wiley & Sons, Inc.

References

Sep 22, 2011·Wiley Interdisciplinary Reviews. RNA·Robert B Darnell
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Jun 6, 2012·Annual Review of Biochemistry·John L Rinn, Howard Y Chang
Jul 4, 2013·Current Protocols in Molecular Biology·Nicholas T IngoliaJonathan S Weissman
Jul 6, 2013·Cell·Igor Ulitsky, David P Bartel
Aug 28, 2014·Cell Reports·Nicholas T IngoliaJonathan S Weissman
Feb 24, 2016·Nature Biotechnology·Zhe JiKevin Struhl
Jun 6, 2017·Methods : a Companion to Methods in Enzymology·Nicholas J McGlincy, Nicholas T Ingolia
Sep 5, 2018·Current Protocols in Molecular Biology·Zhe Ji

❮ Previous
Next ❯

Citations

Nov 17, 2019·Nucleic Acids Research·Malgorzata Kwasniak-OwczarekHanna Janska
Nov 25, 2019·Wiley Interdisciplinary Reviews. RNA·Stephen J KiniryPavel V Baranov
Feb 2, 2021·Frontiers in Oncology·Jiani XingLihong Wang

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Environmental Science & Technology
Current Protocols in Nucleic Acid Chemistry
Line Dahl Poulsen, Jeppe Vinther
© 2022 Meta ULC. All rights reserved