Chemical crosslinking enhances RNA immunoprecipitation for efficient identification of binding sites of proteins that photo-crosslink poorly with RNA
Open accessAbstract
In eukaryotic cells, proteins that associate with RNA regulate its activity to control cellular function. To fully illuminate the basis of RNA function, it is essential to identify such RNA-associated proteins, their mode of action on RNA, and their preferred RNA targets and binding sites. By analyzing catalogs of human RNA-associated proteins defined by ultraviolet light (UV)-dependent and -independent approaches, we classify these proteins into two major groups: (i) the widely recognized RNA binding proteins (RBPs), which bind RNA directly and UV-crosslink efficiently to RNA, and (ii) a new group of RBP-associated factors (RAFs), which bind RNA indirectly via RBPs and UV-crosslink poorly to RNA. As the UV crosslinking and immunoprecipitation followed by sequencing (CLIP-seq) approach will be unsuitable to identify binding sites of RAFs, we show that formaldehyde crosslinking stabilizes RAFs within ribonucleoproteins to allow for their immunoprecipitation under stringent conditions. Using an RBP (CASC3) and an RAF (RNPS1) within the exon junction complex (EJC) as examples, we show that formaldehyde crosslinking combined with RNA immunoprecipitation in tandem followed by sequencing (xRIPiT-seq) far exceeds CLIP-seq to identify binding sites of RNPS1. xRIPiT-seq reveals that RNPS1 occupancy is increased on exons immediately upstream of strong recursively spliced exons, which depend on the EJC for their inclusion.
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The transfer and isolation step by itself drives a dramatic reduction in experimental yield.
“However, in addition to being complex for novice users and limiting scalability and automated handling, we and others have observed that this transfer and isolation step by itself drives a dramatic reduction in experimental yield, and multiple recent modified RBP immunoprecipitation protocols have been described which leave out this step (Gay et al., 2018;Ilik et al., 2020;Patton et al., 2020).”
From Scalable and deep profiling of mRNA targets for individual microRNAs with chimeric eCLIP (2022) · cites this paper as Patton et al., 2020
The Materials and Methods section describes immunoprecipitation and sample handling, while the Results discuss protein solubility under different crosslinking conditions; neither reports a yield loss caused by a transfer-and-isolation step. Searches for membrane transfer, gel isolation, and yield or recovery found no passage addressing that claim in our copy. (LLM, conf=0.73)
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- Authors
- Patton, R. D., Sanjeev, M., Woodward, L. A., Mabin, J. W., Bundschuh, R., & Singh, G.
- Affiliations
- The Ohio State University (US)
- Venue
- RNA
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2020-05-28
- Volume
- 26
- Issue
- 9
- Pages
- 1216-1233
- ISSN
- 1355-8382 (ISSN-L)
- 1469-9001
- PMC
- PMC7430673
- OpenAlex
- W3031060555
- Cited by
- 46
- References
- 57
- Citations by year
- 2026: 4 · 2025: 2 · 2024: 9 · 2023: 13 · 2022: 12 · 2021: 5 · 2020: 1
- FWCI
- 2.51
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- cc-by-nc
- Locations
- RNA (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Ohio Supercomputer Center
- National Institutes of Health (R01-GM120209)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- RNA-binding proteins, formaldehyde crosslinking, RNA immunoprecipitation, CLIP-seq, RNPS1, exon junction complex, protein-RNA binding sites, UV crosslinking, ribonucleoprotein, RNA splicing
- MeSH terms
- Binding Sites, Cell Line, Eukaryotic Cells, Exons, Humans, Protein Binding, Ribonucleoproteins, RNA, RNA Splicing, RNA-Binding Proteins, Immunoprecipitation, HEK293 Cells, Transcriptome
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