Protein-mRNA interactome capture: cartography of the mRNP landscape

F1000Research
Sean P Ryder

Abstract

RNA-binding proteins play a variety of roles in cellular physiology. Some regulate mRNA processing, mRNA abundance, and translation efficiency. Some fight off invader RNA through small RNA-driven silencing pathways. Others sense foreign sequences in the form of double-stranded RNA and activate the innate immune response. Yet others, for example cytoplasmic aconitase, act as bi-functional proteins, processing metabolites in one conformation and regulating metabolic gene expression in another. Not all are involved in gene regulation. Some play structural roles, for example, connecting the translational machinery to the endoplasmic reticulum outer membrane. Despite their pervasive role and relative importance, it has remained difficult to identify new RNA-binding proteins in a systematic, unbiased way. A recent body of literature from several independent labs has defined robust, easily adaptable protocols for mRNA interactome discovery. In this review, I summarize the methods and review some of the intriguing findings from their application to a wide variety of biological systems.

References

Dec 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·M C KennedyH Beinert
Aug 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·D J HaileR D Klausner
Nov 15, 1991·Proceedings of the National Academy of Sciences of the United States of America·S KaptainR D Klausner
May 4, 1990·Cell·C F Lehner, P H O'Farrell
Dec 15, 1986·Biochemical and Biophysical Research Communications·A FavreC Salet
Aug 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·T A RouaultR D Klausner
Jul 1, 1994·Molecular Biology Reports·E J Sontheimer
Jan 1, 1993·Molecular Biology of the Cell·R D Klausner, T A Rouault
Aug 6, 1996·Proceedings of the National Academy of Sciences of the United States of America·D J SenGuptaM Wickens
Dec 29, 1999·Human Mutation·A HamoshV A McKusick
Feb 19, 2000·Current Opinion in Structural Biology·K S Gajiwala, S K Burley
Sep 6, 2002·The Journal of Cell Biology·Stephen L RogersRonald D Vale
Apr 22, 2003·Genes & Development·Hang Shi, Rui-Ming Xu
Jun 5, 2003·Current Biology : CB·Chi-Kong LauGregory D Van Duyne
Apr 30, 2005·Trends in Endocrinology and Metabolism : TEM·Song-Yu YangHorst Schulz
Jun 21, 2005·Current Opinion in Structural Biology·Traci M Tanaka Hall
Nov 30, 2005·Methods : a Companion to Methods in Enzymology·Jernej UleRobert B Darnell
Dec 24, 2005·Canadian Journal of Anaesthesia = Journal Canadien D'anesthésie·Deven ChandraJohn Usher
Jul 10, 2007·Molecular Genetics and Metabolism·Song-Yu YangDavid Miller
Mar 11, 2008·Nature Structural & Molecular Biology·Matthew T MillerTraci M Tanaka Hall
Mar 28, 2008·Critical Reviews in Biochemistry and Molecular Biology·Brian M Farley, Sean P Ryder
Jun 3, 2008·Current Opinion in Structural Biology·Antoine CléryFrédéric H-T Allain
Oct 7, 2008·Nucleic Acids Research·UNKNOWN UniProt Consortium
Nov 4, 2008·Nature·Donny D LicatalosiRobert B Darnell
Nov 5, 2008·Methods in Molecular Biology·Kirk B Jensen, Robert B Darnell
Jun 10, 2009·Nature Reviews. Genetics·Eran Segal, Jonathan Widom
Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Colin C ConineCraig C Mello
Apr 22, 2010·Science Signaling·Muhammad Munir
May 11, 2010·Trends in Biochemical Sciences·Christian U StirnimannChristoph W Müller
Jun 18, 2010·Trends in Biochemical Sciences·Matthias W Hentze, Thomas Preiss

❮ Previous
Next ❯

Citations

Jun 17, 2018·FEBS Letters·Waleed S Albihlal, André P Gerber
Dec 7, 2018·F1000Research·Brigitte SchönbergerBjörn Voß
Dec 23, 2019·Structure·Lyudmila Dimitrova-PaternogaJanosch Hennig
Nov 14, 2021·Nature Communications·Ines C Osma-GarciaManuel D Diaz-Muñoz

❮ Previous
Next ❯

Methods Mentioned

BETA
RAP
immunoprecipitation
RNA-seq
iCLIP
CLIP
PAR-CLIP

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.