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GoldCLIP: Gel-omitted Ligation-dependent CLIP.
- Source :
-
Genomics, proteomics & bioinformatics [Genomics Proteomics Bioinformatics] 2018 Apr; Vol. 16 (2), pp. 136-143. Date of Electronic Publication: 2018 Apr 28. - Publication Year :
- 2018
-
Abstract
- Protein-RNA interaction networks are essential to understand gene regulation control. Identifying binding sites of RNA-binding proteins (RBPs) by the UV-crosslinking and immunoprecipitation (CLIP) represents one of the most powerful methods to map protein-RNA interactions in vivo. However, the traditional CLIP protocol is technically challenging, which requires radioactive labeling and suffers from material loss during PAGE-membrane transfer procedures. Here we introduce a super-efficient CLIP method (GoldCLIP) that omits all gel purification steps. This nonisotopic method allows us to perform highly reproducible CLIP experiments with polypyrimidine tract-binding protein (PTB), a classical RBP in human cell lines. In principle, our method guarantees sequencing library constructions, providing the protein of interest can be successfully crosslinked to RNAs in living cells. GoldCLIP is readily applicable to diverse proteins to uncover their endogenous RNA targets.<br /> (Copyright © 2018 The Authors. Production and hosting by Elsevier B.V. All rights reserved.)
- Subjects :
- Binding Sites
Cell Line
Heterogeneous-Nuclear Ribonucleoproteins isolation & purification
Heterogeneous-Nuclear Ribonucleoproteins metabolism
Humans
Polypyrimidine Tract-Binding Protein isolation & purification
Polypyrimidine Tract-Binding Protein metabolism
RNA isolation & purification
RNA-Binding Proteins isolation & purification
Immunoprecipitation methods
RNA metabolism
RNA-Binding Proteins metabolism
Subjects
Details
- Language :
- English
- ISSN :
- 2210-3244
- Volume :
- 16
- Issue :
- 2
- Database :
- MEDLINE
- Journal :
- Genomics, proteomics & bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 29709556
- Full Text :
- https://doi.org/10.1016/j.gpb.2018.04.003