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

Wenkai Yi1,2, Jingyu Li2,3, Xiaoxuan Zhu2,3, Xi Wang1,4, Ligang Fan1,2, Wenju Sun1, Linbu Liao1, Jilin Zhang5, Xiaoyu Li1,2, Jing Ye6, Fulin Chen1, Jussi Taipale5,7, Kui Ming Chan8,9, Liang Zhang10,11, Jian Yan12,13

  1. School of Medicine, Northwest University, Xi'an, China.
  2. Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China.
  3. Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
  4. Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany.
  5. Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
  6. Department of Pathology, The Fourth Military Medical University, Xi'an, China.
  7. Department of Biochemistry, University of Cambridge, Cambridge, UK.
  8. Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China. ming.chan@cityu.edu.hk.
  9. Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China. ming.chan@cityu.edu.hk.
  10. Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China. liangzhang.28@cityu.edu.hk.
  11. Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China. liangzhang.28@cityu.edu.hk.
  12. School of Medicine, Northwest University, Xi'an, China. jian.yan@cityu.edu.hk.
  13. Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China. jian.yan@cityu.edu.hk.

Abstract

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.

Presented By Jingyu Li | ORCID iD

GenomicsNicholas Liao2020-07 (Jul)