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TALEN-mediated enhancer knockout influences TNFAIP3 gene expression and mimics a molecular phenotype associated with systemic lupus erythematosus

Genes & Immunity volume 17, pages 165–170 (2016)Cite this article

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Abstract

Linkage disequilibrium poses a major challenge to the functional characterization of specific disease-associated susceptibility variants. Precision genome-editing technologies have provided new opportunities to address this challenge. As proof of concept, we employed TALEN (transcription activation-like effector nuclease)-mediated genome editing to specifically disrupt the TT>A enhancer region to mimic candidate causal variants identified in the systemic lupus erythematosus-associated susceptibility gene, tumor necrosis factor-α-induced protein 3 (TNFAIP3), in an isogenic HEK293T cell line devoid of other linkage disequilibrium-associated variants. Targeted disruption of the TT>A enhancer impaired its interaction with the TNFAIP3 promoter by long-range DNA looping, thereby reducing TNFAIP3 gene expression. Loss of TNFAIP3 mRNA and its encoded protein, A20, impaired tumor necrosis factor-α-induced receptor-mediated downregulation of nuclear factor-κB signaling, a hallmark of autoimmunity. Results demonstrate that the TT>A enhancer variants contribute to causality and function independently of other variants to disrupt TNFAIP3 expression. Furthermore, we believe this approach can be implemented to independently examine other candidate casual variants in the future.

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Acknowledgements

This work was supported by grants from the National Institutes of Health 5 R01 AR056360-05, 5 R01 AR063124-04 and P30 GM110766.

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Authors and Affiliations

  1. Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA

    S Wang, F Wen, K L Tessneer & P M Gaffney

  2. Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China

    S Wang

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

    S Wang

  4. Feinberg School of Medicine, Northwestern University, Chicago, IL, USA

    F Wen

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  1. S Wang
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Correspondence to P M Gaffney.

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Wang, S., Wen, F., Tessneer, K. et al. TALEN-mediated enhancer knockout influences TNFAIP3 gene expression and mimics a molecular phenotype associated with systemic lupus erythematosus. Genes Immun 17, 165–170 (2016). https://doi.org/10.1038/gene.2016.4

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