Methods to study RNA-protein interactions

Nature Methods
Muthukumar RamanathanPaul A Khavari

Abstract

Noncoding RNA sequences, including long noncoding RNAs, small nucleolar RNAs, and untranslated mRNA regions, accomplish many of their diverse functions through direct interactions with RNA-binding proteins (RBPs). Recent efforts have identified hundreds of new RBPs that lack known RNA-binding domains, thus underscoring the complexity and diversity of RNA-protein complexes. Recent progress has expanded the number of methods for studying RNA-protein interactions in two general categories: approaches that characterize proteins bound to an RNA of interest (RNA-centric), and those that examine RNAs bound to a protein of interest (protein-centric). Each method has unique strengths and limitations, which makes it important to select optimal approaches for the biological question being addressed. Here we review methods for the study of RNA-protein interactions, with a focus on their suitability for specific applications.

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Methods Mentioned

BETA
pulldown
in vitro methods
pull down
antisense oligonucleotides
ChIRP
transfection
chemical modification
cross-linking immunoprecipitation
CLIP-seq
CLIP

Software Mentioned

RaPID
NumPy
statsmodels
Jupyter
SciPy
eCLIP
HTSeq
Puf2p
CLIP
PAR

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