easyCLIP analysis of RNA-protein interactions incorporating absolute quantification

Douglas F. Porter, Weili Miao, Xue Yang, Grant A. Goda, Andrew L. Ji, Laura K. H. Donohue, Maria M. Aleman, Daniel Dominguez and Paul A. Khavari ()
Additional contact information
Douglas F. Porter: Stanford University
Weili Miao: Stanford University
Xue Yang: Stanford University
Grant A. Goda: University of North Carolina at Chapel Hill
Andrew L. Ji: Stanford University
Laura K. H. Donohue: Stanford University
Maria M. Aleman: University of North Carolina at Chapel Hill
Daniel Dominguez: University of North Carolina at Chapel Hill
Paul A. Khavari: Stanford University

Nature Communications, 2021, vol. 12, issue 1, 1-16

Abstract: Abstract Quantitative criteria to identify proteins as RNA-binding proteins (RBPs) are presently lacking, as are criteria to define RBP target RNAs. Here, we develop an ultraviolet (UV) cross-linking immunoprecipitation (CLIP)-sequencing method, easyCLIP. easyCLIP provides absolute cross-link rates, as well as increased simplicity, efficiency, and capacity to visualize RNA libraries during sequencing library preparation. Measurement of >200 independent cross-link experiments across >35 proteins identifies an RNA cross-link rate threshold that distinguishes RBPs from non-RBPs and defines target RNAs as those with a complex frequency unlikely for a random protein. We apply easyCLIP to the 33 most recurrent cancer mutations across 28 RBPs, finding increased RNA binding per RBP molecule for KHDRBS2 R168C, A1CF E34K and PCBP1 L100P/Q cancer mutations. Quantitating RBP-RNA interactions can thus nominate proteins as RBPs and define the impact of specific disease-associated RBP mutations on RNA association.

Date: 2021
References: Add references at CitEc
Citations: View citations in EconPapers (1)

Downloads: (external link)
https://www.nature.com/articles/s41467-021-21623-4 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-21623-4

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-021-21623-4

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().