Protocol Executing cell-specific cross-linking immunoprecipitation and sequencing (seCLIP) in C. elegans

The single-end enhanced cross-linking immunoprecipitation (seCLIP) method is well suited for efficient and unbiased transcriptome-wide interrogation of RNA-binding protein (RBP) interaction sites. Here, we provide a protocol for executing cell-specific seCLIP for any desired RBP in Caenorhabditis elegans. We begin with steps and recommendations for transgene construction and Cas9-mediated chromosomal integration. We provide detailed procedures for isolation of RBP-associated RNA fragments, subsequent library preparation, and sequencing. We further discuss best practices for data analysis, interpretation of results, and troubleshooting. For complete details on the use and execution of this protocol, please refer to Blazie et al. (2021).1

Automated summary

The seCLIP method is suitable for studying the interaction sites between RNA-binding proteins (RBPs) and the transcriptome. This article provides a protocol for executing cell-specific seCLIP in Caenorhabditis elegans, including steps such as transgene construction, isolation of RBP-associated RNA fragments, library preparation, and sequencing.