TY  - JOUR
TI  - Affinity Pulldown of Biotinylated RNA for Detection of Protein-RNA Complexes
AU  - Panda, Amaresh C.
AU  - Martindale , Jennifer L.
AU  - Gorospe, Myriam 
VL  - 6
IS  - 24
PY  - 2016
DA  - 2016/12/20
SP  - e2062
C1  - Bio-protocol 2016;6:e2062
DO  - 10.21769/BioProtoc.2062
UR  - https://doi.org/10.21769/BioProtoc.2062
AB  - RNA-binding proteins (RBPs) have recently emerged as crucial players in the regulation of gene expression. The interactions of RBPs with target mRNAs control the levels of gene products by altering different regulatory steps, including pre-mRNA splicing and maturation, nuclear mRNA export, and mRNA stability and translation (Glisovic et al., 2008). There are several methodologies available today to identify RNAs bound to specific RBPs; some detect only recombinant molecules in vitro, others detect recombinant and endogenous molecules, while others detect only endogenous molecules. Examples include systematic evolution of ligands by exponential enrichment (SELEX), biotinylated RNA pulldown assay, RNA immunoprecipitation (RIP) assay, electrophoretic mobility shift assay (EMSA), RNA footprinting analysis, and various UV crosslinking and immunoprecipitation (CLIP) methods such as CLIP, PAR-CLIP, and iCLIP (Popova et al., 2015). Here, we describe a simple and informative method to study and identify the RNA region of interaction between an RBP and its target transcript (Panda et al., 2014 and 2016). Its reproducibility and ease of use make this protocol a fast and useful method to identify interactions between RBPs and specific RNAs.
KW  - Tagged RNA
KW  - RNA-binding proteins
KW  - Ribonucleoprotein complex
KW  - Biotin pulldown
KW  - in vitro transcription
JF  - Bio-protocol
SN  - 2331-8325
PB  - Bio-protocol LLC.
BIO101  - False