TY - JOUR
T1 - Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding
AU - Johnston, Andrew D.
AU - Simões-Pires, Claudia A.
AU - Thompson, Taylor V.
AU - Suzuki, Masako
AU - Greally, John M.
N1 - Funding Information:
The authors thank the following Einstein core facilities for their expertise: the Epige-nomics Shared Facility, the Flow Cytometry Core Facility, the Computational Genomics Core Facility, and the Genomics Core Facility. Michela Ranieri from the laboratory of Antonio Di Cristofano (Einstein) is also thanked for her help. The feedback of colleagues at the New York Genome Center, especially the laboratory of Tuuli Lappalainen, is also gratefully acknowledged. A.D.J. was supported by Einstein’s Medical Scientist Training Program NIH NIGMS T32 GM007288. C.A.S.-P. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 750190.
Publisher Copyright:
© 2019, The Author(s).
PY - 2019/12/1
Y1 - 2019/12/1
N2 - Functional variants in the genome are usually identified by their association with local gene expression, DNA methylation or chromatin states. DNA sequence motif analysis and chromatin immunoprecipitation studies have provided indirect support for the hypothesis that functional variants alter transcription factor binding to exert their effects. In this study, we provide direct evidence that functional variants can alter transcription factor binding. We identify a multifunctional variant within the TBC1D4 gene encoding a canonical NFκB binding site, and edited it using CRISPR-Cas9 to remove this site. We show that this editing reduces TBC1D4 expression, local chromatin accessibility and binding of the p65 component of NFκB. We then used CRISPR without genomic editing to guide p65 back to the edited locus, demonstrating that this re-targeting, occurring ~182 kb from the gene promoter, is enough to restore the function of the locus, supporting the central role of transcription factors mediating the effects of functional variants.
AB - Functional variants in the genome are usually identified by their association with local gene expression, DNA methylation or chromatin states. DNA sequence motif analysis and chromatin immunoprecipitation studies have provided indirect support for the hypothesis that functional variants alter transcription factor binding to exert their effects. In this study, we provide direct evidence that functional variants can alter transcription factor binding. We identify a multifunctional variant within the TBC1D4 gene encoding a canonical NFκB binding site, and edited it using CRISPR-Cas9 to remove this site. We show that this editing reduces TBC1D4 expression, local chromatin accessibility and binding of the p65 component of NFκB. We then used CRISPR without genomic editing to guide p65 back to the edited locus, demonstrating that this re-targeting, occurring ~182 kb from the gene promoter, is enough to restore the function of the locus, supporting the central role of transcription factors mediating the effects of functional variants.
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U2 - 10.1038/s41467-019-11412-5
DO - 10.1038/s41467-019-11412-5
M3 - Article
C2 - 31375681
AN - SCOPUS:85071147714
SN - 2041-1723
VL - 10
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 3472
ER -