Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding

Andrew D. Johnston, Claudia A. Simões-Pires, Taylor V. Thompson, Masako Suzuki, John M. Greally

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Number of pages1
JournalNature communications
Volume10
Issue number1
DOIs
StatePublished - Aug 2 2019

Fingerprint

chromatin
Clustered Regularly Interspaced Short Palindromic Repeats
Chromatin
editing
Transcription Factors
loci
genes
deoxyribonucleic acid
Genes
Nucleotide Motifs
Gene encoding
methylation
genome
Chromatin Immunoprecipitation
gene expression
DNA sequences
DNA Methylation
DNA Sequence Analysis
Gene expression
coding

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding. / Johnston, Andrew D.; Simões-Pires, Claudia A.; Thompson, Taylor V.; Suzuki, Masako; Greally, John M.

In: Nature communications, Vol. 10, No. 1, 02.08.2019.

Research output: Contribution to journalArticle

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