GoldCLIP: Gel-omitted Ligation-dependent CLIP

Protein-RNA interaction networks are essential to understand gene regulation control. Identifying the binding sites of RNA-binding proteins (RBPs) by CLIP (UV-crosslinking and immunoprecipitation) represents one of the most powerful methods to map in vivo protein-RNA interactions. 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 allowed us to perform highly reproducible CLIP experiments with classical RBP such as PTB 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 factors to uncover their endogenous targets. Gel-omitted Ligation-dependent CLIP applied to characterize the in vivo protein-RNA interactions This series includes re-analyzed data from ERP016865; Array Express accession ID: E-MTAB-5027. The re-analyzed data file is: PTB_iCLIP2.bed.gz, available below. This file contains data from all samples in ERP016865. The methods used to produce these CLIP peaks are identical to those listed for the samples in this series.