The CLIP Method to Study Protein-RNA Interactions in Intact Cells and Tissues

TY - CHAP

T1 - The CLIP Method to Study Protein-RNA Interactions in Intact Cells and Tissues

AU - Tollervey, James

AU - Ule, Jernej

PY - 2012/2/2

Y1 - 2012/2/2

N2 - In order to understand the mechanisms by which RNA-binding proteins carry out their functions, it is important to identify where they bind their targets. To facilitate this, the UV-crosslinking and Immunoprecipitation (CLIP) method was developed which allows for in vivo identification of protein-RNA interactions. To identify the sequence of CLIP RNAs, these need to be ligated to adapters and amplified to a cDNA library, which can be an inefficient process that had been improved over the last years. In this chapter, we present the general CLIP protocol and describe how the individual steps in the protocol can be optimized depending on the protein studied and the cell type or tissue used.

AB - In order to understand the mechanisms by which RNA-binding proteins carry out their functions, it is important to identify where they bind their targets. To facilitate this, the UV-crosslinking and Immunoprecipitation (CLIP) method was developed which allows for in vivo identification of protein-RNA interactions. To identify the sequence of CLIP RNAs, these need to be ligated to adapters and amplified to a cDNA library, which can be an inefficient process that had been improved over the last years. In this chapter, we present the general CLIP protocol and describe how the individual steps in the protocol can be optimized depending on the protein studied and the cell type or tissue used.

KW - CLIP

KW - Immunoprecipitation

KW - RNA-protein interaction

KW - UV crosslinking

UR - http://www.scopus.com/inward/record.url?scp=84885508245&partnerID=8YFLogxK

U2 - 10.1002/9783527636778.ch25

DO - 10.1002/9783527636778.ch25

M3 - Chapter

AN - SCOPUS:84885508245

SN - 9783527326068

SP - 268

EP - 278

BT - Alternative pre-mRNA Splicing

PB - Wiley - VCH

ER -