ZFIN ID: ZDB-PUB-181118-22
Identification of common non-coding variants at 1p22 that are functional for non-syndromic orofacial clefting
Liu, H., Leslie, E.J., Carlson, J.C., Beaty, T.H., Marazita, M.L., Lidral, A.C., Cornell, R.A.
Date: 2017
Source: Nature communications   8: 14759 (Journal)
Registered Authors: Cornell, Robert
Keywords: none
MeSH Terms:
  • Alleles
  • Animals
  • Animals, Genetically Modified
  • Biological Assay
  • Chromatin/chemistry
  • Chromosomes, Human, Pair 1/chemistry*
  • Cleft Lip/diagnosis
  • Cleft Lip/genetics*
  • Cleft Lip/pathology
  • Cleft Palate/diagnosis
  • Cleft Palate/genetics*
  • Cleft Palate/pathology
  • Enhancer Elements, Genetic
  • GTPase-Activating Proteins/genetics*
  • GTPase-Activating Proteins/metabolism
  • Gene Expression
  • Genes, Reporter
  • Genetic Loci
  • Genetic Predisposition to Disease*
  • Genome-Wide Association Study
  • Humans
  • Linkage Disequilibrium
  • Luciferases/genetics
  • Luciferases/metabolism
  • Polymorphism, Single Nucleotide
  • Promoter Regions, Genetic
  • Risk Factors
  • Transcription Factors/genetics*
  • Transcription Factors/metabolism
  • Zebrafish
PubMed: 28287101 Full text @ Nat. Commun.
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.