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

Genes and Immunity
Jianfeng WuShaofeng Wang

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.

References

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Citations

Jan 24, 2019·Current Rheumatology Reports·Adam J FikeZiaur S M Rahman
Apr 3, 2020·EMBO Molecular Medicine·Christophe BourgesJames C Lee
Oct 16, 2018·Frontiers in Immunology·Tue W KragstrupBent Deleuran
Aug 18, 2018·Genes and Immunity·Thomas Brunner, Marie-Lise Gougeon
May 19, 2020·Human Molecular Genetics·James DingGisela Orozco
May 22, 2019·Seminars in Cell & Developmental Biology·Desh Deepak SinghSubhash K Tripathi
Jun 8, 2021·Molecular Therapy. Methods & Clinical Development·Eric AlvesPilar Blancafort

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Methods Mentioned

BETA
PCR
transfection

Software Mentioned

Targeter
Chi
UCSC genome browser
TALEN

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