Enhanced Crosslinking Immunoprecipitation (eCLIP): A Method for Efficient RNA-Protein Interaction Analysis

Marketing Dept., | 4 min read
Marketing Dept., | 4 min read

Enhanced Crosslinking Immunoprecipitation (eCLIP) is a cutting-edge technique designed to provide detailed insights into RNA-protein interactions with high efficiency and precision. This blog post explores the eCLIP method, its applications, and how researchers can leverage this technique in their studies.

What is eCLIP?

Enhanced Crosslinking Immunoprecipitation (eCLIP) is an advanced method used to study RNA-protein interactions. It builds upon traditional CLIP techniques by incorporating additional steps that enhance the efficiency and accuracy of RNA-protein interaction mapping. eCLIP allows researchers to identify the binding sites of RNA-binding proteins (RBPs) across the transcriptome, providing a comprehensive view of RNA regulation.

The Methodology

The eCLIP method involves several key steps:

  1. Crosslinking: Cells or tissues are treated with ultraviolet (UV) light to crosslink RNA and proteins, creating covalent bonds that stabilize RNA-protein complexes.
  2. Cell Lysis and RNA Fragmentation: The crosslinked cells are lysed, and RNA is fragmented into manageable pieces. This step ensures that only the RNA directly bound to proteins is analyzed.
  3. Immunoprecipitation: Specific antibodies are used to isolate RNA-protein complexes of interest. This step enriches the sample for the RBPs and their associated RNAs.
  4. Library Preparation and Sequencing: The isolated RNA fragments are converted into a cDNA library and sequenced using high-throughput sequencing technologies. This allows for precise identification of RBP binding sites.

Learning More with JoVE

For researchers interested in mastering the eCLIP technique, JoVE (Journal of Visualized Experiments) offers comprehensive resources. The article "Enhanced Crosslinking Immunoprecipitation (eCLIP) Method for Efficient RNA-Protein Interaction Analysis" provides an in-depth guide to the eCLIP method, including detailed protocols and practical tips.

Article Citation

  • Xu, Q., Wang, C., Ling, L., Yue, Q., Liu, M., Zhang, S., Fu, K., Ye, L., Zheng, K. Enhanced Crosslinking Immunoprecipitation (eCLIP) Method for Efficient Identification of Protein-bound RNA in Mouse Testis. J. Vis. Exp. (147), e59681, doi:10.3791/59681 (2019).


Visit JoVE.com to access this article and explore other valuable resources. JoVE is an essential tool for scientists and students seeking to understand and apply advanced techniques in their research.

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