CRISPR-assisted detection of RNA–protein interactions in living cells

• Published in: Nature methods Vol. 17; no. 7; pp. 685 - 688
• Main Authors: Yi, Wenkai, Li, Jingyu, Zhu, Xiaoxuan, Wang, Xi, Fan, Ligang, Sun, Wenju, Liao, Linbu, Zhang, Jilin, Li, Xiaoyu, Ye, Jing, Chen, Fulin, Taipale, Jussi, Chan, Kui Ming, Zhang, Liang, Yan, Jian
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.07.2020; Nature Publishing Group
• Subjects: 631/1647/2067; 631/1647/2210; 631/1647/2217; 631/208/191; Animals; Binders; Binding; Binding proteins; Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Biotin; Brief Communication; Cells (biology); Clustered Regularly Interspaced Short Palindromic Repeats; CRISPR; DNA-Binding Proteins - metabolism; HEK293 Cells; Humans; Labeling; Life Sciences; Ligases; Medicin och hälsovetenskap; Non-coding RNA; Protein binding; Protein interaction; Proteins; Proteomics; Ribonucleic acid; RNA; RNA, Long Noncoding - metabolism; RNA-binding protein; RNA-Binding Proteins - metabolism; TATA-Binding Protein Associated Factors - metabolism; Transcription Factors - metabolism; China
• ISSN: 1548-7091; 1548-7105; 1548-7105
• DOI: 10.1038/s41592-020-0866-0

We have developed CRISPR-assisted RNA–protein interaction detection method (CARPID), which leverages CRISPR–CasRx-based RNA targeting and proximity labeling to identify binding proteins of specific long non-coding RNAs (lncRNAs) in the native cellular context. We applied CARPID to the nuclear lncRNA XIST, and it captured a list of known interacting proteins and multiple previously uncharacterized binding proteins. We generalized CARPID to explore binders of the lncRNAs DANCR and MALAT1, revealing the method’s wide applicability in identifying RNA-binding proteins. CARPID uses CRISPR technology to navigate biotin ligase to specific lncRNAs, which allows proximal labeling and thus the querying of RNA–protein interactions in living cells.