Identification of common non-coding variants at 1p22 that are functional for non-syndromic orofacial clefting

Huan Liu, Elizabeth J. Leslie, Jenna C. Carlson, Terri H. Beaty, Mary L. Marazita, Andrew C. Lidral and Robert A. Cornell ()
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Huan Liu: College of Medicine, University of Iowa
Elizabeth J. Leslie: Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh
Jenna C. Carlson: Graduate School of Public Health, University of Pittsburgh
Terri H. Beaty: Bloomberg School of Public Health, Johns Hopkins University
Mary L. Marazita: Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh
Andrew C. Lidral: College of Dentistry, University of Iowa
Robert A. Cornell: College of Medicine, University of Iowa

Nature Communications, 2017, vol. 8, issue 1, 1-13

Abstract: Abstract Genome-wide association studies (GWAS) do not distinguish between single nucleotide polymorphisms (SNPs) that are causal and those that are merely in linkage-disequilibrium with causal mutations. Here we describe a versatile, functional pipeline and apply it to SNPs at 1p22, a locus identified in several GWAS for non-syndromic cleft lip with or without cleft palate (NS CL/P). First we amplified DNA elements containing the ten most-highly risk-associated SNPs and tested their enhancer activity in vitro, identifying three SNPs with allele-dependent effects on such activity. We then used in vivo reporter assays to test the tissue-specificity of these enhancers, chromatin configuration capture to test enhancer–promoter interactions, and genome editing in vitro to show allele-specific effects on ARHGAP29 expression and cell migration. Our results further indicate that two SNPs affect binding of CL/P-associated transcription factors, and one affects chromatin configuration. These results translate risk into potential mechanisms of pathogenesis.

Date: 2017
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DOI: 10.1038/ncomms14759

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