Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

2012/08/03 by Yoichiro Sugimoto, Julian König, Shobbir Hussain +4 · 7 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · #RNA Research and Splicing #RNA modifications and cancer #RNA and protein synthesis mechanisms #RNA #Immunoprecipitation #Complementary DNA #Nucleotide #RNA-binding protein #Biology #Computational biology #Molecular biology #Protein–protein interaction #Uridine #Genetics #Chemistry #Gene

paper · pdf · doi:10.1186/gb-2012-13-8-r67

openalex publication_date 2012/08/03 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01

Abstract

UV cross-linking and immunoprecipitation (CLIP) and individual-nucleotide resolution CLIP (iCLIP) are methods to study protein-RNA interactions in untreated cells and tissues. Here, we analyzed six published and two novel data sets to confirm that both methods identify protein-RNA cross-link sites, and to identify a slight uridine preference of UV-C-induced cross-linking. Comparing Nova CLIP and iCLIP data revealed that cDNA deletions have a preference for TTT motifs, whereas iCLIP cDNA truncations are more likely to identify clusters of YCAY motifs as the primary Nova binding sites. In conclusion, we demonstrate how each method impacts the analysis of protein-RNA binding specificity.

Citations

• Characterization and Functional Implications of the RNA Binding Properties of Nuclear Factor TDP-43, a Novel Splicing Regulator ofCFTR Exon 9
• HITS-CLIP yields genome-wide insights into brain alternative RNA processing
• Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP
• iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
• Characterizing the RNA targets and position-dependent splicing regulation by TDP-43

Cited by

• NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs
• Advances in CLIP Technologies for Studies of Protein-RNA Interactions
• Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis
• Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes
• CLIP and complementary methods
• Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo
• Cross-linking immunoprecipitation [wikipedia]