Protocol for detecting RBM33-binding sites in HEK293T cells using PAR-CLIP-seq

STAR Protoc. 2024 Mar 15;5(1):102855. doi: 10.1016/j.xpro.2024.102855. Epub 2024 Jan 31.


RNA-binding proteins (RBPs) regulate gene expression both co-transcriptionally and post-transcriptionally. Here, we provide a protocol for photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation followed by next-generation sequencing (PAR-CLIP-seq). PAR-CLIP-seq is a transcriptome-scale technique for identifying in vivo binding sites of RBPs at the single-nucleotide level. We detail procedures for the establishment of FLAG-RBM33 stable cell line, the sequencing library preparation, and the data analysis.

Keywords: Bioinformatics; Cell Biology; Molecular Biology.

MeSH terms

  • Binding Sites
  • Chromatin Immunoprecipitation Sequencing*
  • HEK293 Cells
  • Humans
  • RNA-Binding Proteins* / metabolism
  • Transcriptome


  • RNA-Binding Proteins