JOURNAL OF SHANGHAI JIAOTONG UNIVERSITY (MEDICAL SCIENCE) ›› 2021, Vol. 41 ›› Issue (1): 8-15.doi: 10.3969/j.issn.1674-8115.2021.01.002

• Basic research • Previous Articles     Next Articles

Application of CRISPR/Cas9-mediated homologous recombination to the functional study of disease-associated genetic variants located in non-coding region

Ning XU(), Tian ZHOU, Guo-jun HOU, Nan SHEN, Yuan-jia TANG()   

  1. Department of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine; Shanghai Institute of Rheumatology, Shanghai 200127, China
  • Online:2021-01-28 Published:2021-02-22
  • Contact: Yuan-jia TANG;
  • Supported by:
    Funding Information] National Natural Science Foundation of China(81871287);Innovative Research Team of High-Level Local Universities in Shanghai(SSMU-ZDCX20180100)

Abstract: Objective

·To take the systemic lupus erythematosus (SLE)-associated single nucleotide polymorphism (SNP) rs1978421 reported in the genome-wide association study (GWAS) as an example, and establish the research strategy for the functional study of disease-associated genetic variants located in the non-coding region through clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9) system.


·Single guide RNA (sgRNA) was designed for SNP rs1978421. T7 endonuclease Ⅰ (T7E Ⅰ) experiment was used to verify the cleavage efficiency of sgRNA in HEK293T cells. The homologous recombinant template and expression plasmid of Cas9-green fluorescent protein (GFP)/sgRNA were transfected into U-937 cells by electroporation transfection method. GFP positive U-937 single cells were sorted by flow cytometry, and the cells were cultured for the following 14 days. Then the genotype identification was carried out. After the homologous recombinant cell clones were screened, quantitative real-time PCR (qPCR) was used to quantify the upstream and downstream genes of rs1978421 within 2 Mb and miR-146a, and the effects of different alleles of rs1978421 on the expression of miR-146a and its surrounding genes were analyzed.


·T7E Ⅰ assay showed that about 24% of the total rs1978421 sites in HEK293T were cleaved. In homologous recombination experiment of the U-937 cells, a total of 141 cell lines were obtained and only six were successful, while the ratio of homologous recombination was 4.3%. qPCR showed that there was no significant difference in the expression of miR-146a and the detected genes between wild type TT and homologous recombinant CC in the U-937 cells (all P>0.05).


·SNP rs1978421 has no regulatory effect on the surrounding genes within 2 Mb and miR-146a. However, this study proves the feasibility of CRISPR-mediated homologous recombination technology for the functional study of SNP sites in the non-coding regions.

Key words: clustered regularly interspaced short palindromic repeats (CRISPR), homologous recombination, genome-wide association study (GWAS), single nucleotide polymorphism (SNP)

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