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CRISPR/cas9 mediated knockout of an intergenic variant rs6927172 identified IL-20RA as a new risk gene for multiple autoimmune diseases

Genes & Immunity volume 20, pages 103–111 (2019)Cite this article

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Abstract

Genetic variants near the tumor necrosis factor-α-induced protein 3 gene (TNFAIP3) at the chromosomal region 6q23 demonstrated significant associations with multiple autoimmune diseases. The signals of associations have been explained to the TNFAIP3 gene, the most likely causal gene. In this study, we employed CRISPR/cas9 genome-editing tool to generate cell lines with deletions including a candidate causal variant, rs6927172, at 140 kb upstream of the TNFAIP3 gene. Interestingly, we observed alterations of multiple genes including IL-20RA encoding a subunit of the receptor for interleukin 20. Using Electrophoretic mobility shift assay (EMSA), Western blotting, and chromatin conformation capture we characterized the molecular mechanism that the DNA element carrying the variant rs6927172 influences expression of IL-20RA and TNFAIP3 genes. Additionally, we developed a new use of the transcription activator-like effector (TALE) to study the role of the variant in regulating expressions of its target genes. In summary, we generated deletion knockouts that included the candidate causal variant rs6927172 in HEK293T cells provided new evidence and mechanism for IL-20RA gene as a risk factor for multiple autoimmune diseases.

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Acknowledgements

We would like to acknowledge the Faculty of the College of Life Sciences Genomics Facility and the assistance given by IT Services and the use of the Computational Shared Facility at the Jilin University.

Funding

Funding

Support for this work was obtained from the National Natural Science Foundation of China grants 31670795 and the start funding from The First Hospital of Jilin University.

Author information

Author notes

  1. These authors contributed equally: Jianfeng Wu, Sirui Yang.

  2. These authors jointly supervised this work: Jiaao Yu, Liankun Sun, Shaofeng Wang.

Authors and Affiliations

  1. The Institute of Epigenetic Medicine, The First Hospital of Jilin University, Changchun, China

    Jianfeng Wu, Di Yu, Wenjing Gao, Xianjun Liu & Shaofeng Wang

  2. College of Basic Medicine, The Jilin University, Changchun, China

    Jianfeng Wu & Liankun Sun

  3. The Institute of Pediatrics, The First Hospital of Jilin University, Changchun, China

    Sirui Yang & Shaofeng Wang

  4. The Center of Research, The Second Hospital of Jilin University, Changchun, China

    Kun Zhang

  5. The College of Life Sciences, The Jilin University, Changchun, China

    Xueqi Fu

  6. Department of Infectious Diseases, The First Hospital of Jilin University, Changchun, China

    Wanguo Bao & Kaiyu Zhang

  7. Department of Burn Surgery, The First Hospital of Jilin University, Changchun, China

    Jiaao Yu

Authors
  1. Jianfeng Wu
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Contributions

JW, SY, DY, WG, XL, KZ, XF, WB, KZ, and JY performed experiments and contributed to the writing of the paper. JY, LS, and SW designed experiments and SW wrote the paper. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Shaofeng Wang.

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The authors declare that they have no conflict of interest.

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Wu, J., Yang, S., Yu, D. et al. CRISPR/cas9 mediated knockout of an intergenic variant rs6927172 identified IL-20RA as a new risk gene for multiple autoimmune diseases. Genes Immun 20, 103–111 (2019). https://doi.org/10.1038/s41435-018-0011-6

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  • DOI: https://doi.org/10.1038/s41435-018-0011-6

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