Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP
- Resource Type
- Article
- Authors
- Lorenz, Daniel A.; Her, Hsuan-Lin; Shen, Kylie A.; Rothamel, Katie; Hutt, Kasey R.; Nojadera, Allan C.; Bruns, Stephanie C.; Manakov, Sergei A.; Yee, Brian A.; Chapman, Karen B.; Yeo, Gene W.
- Source
- Nature Methods; January 2023, Vol. 20 Issue: 1 p65-69, 5p
- Subject
- Language
- ISSN
- 15487091; 15487105
Ultraviolet crosslinking and immunoprecipitation (CLIP) methodologies enable the identification of RNA binding sites of RNA-binding proteins (RBPs). Despite improvements in the library preparation of RNA fragments, the enhanced CLIP (eCLIP) protocol requires 4 days of hands-on time and lacks the ability to process several RBPs in parallel. We present a new method termed antibody-barcode eCLIP that utilizes DNA-barcoded antibodies and proximity ligation of the DNA oligonucleotides to RBP-protected RNA fragments to interrogate several RBPs simultaneously. We observe performance comparable with that of eCLIP with the advantage of dramatically increased scaling while maintaining the same material requirement of a single eCLIP experiment.