Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip.
Previously we have shown that nonsyndromic cleft lip with or without cleft palate (NSCL/P) is strongly associated with SNPs in IRF6 (interferon regulatory factor 6). Here, we use multispecies sequence comparisons to identify a common SNP (rs642961, G>A) in a newly identified IRF6 enhancer. The A allele is significantly overtransmitted (P = 1 x 10(-11)) in families with NSCL/P, in particular those with cleft lip but not cleft palate. Further, there is a dosage effect of the A allele, with a relative risk for cleft lip of 1.68 for the AG genotype and 2.40 for the AA genotype. EMSA and ChIP assays demonstrate that the risk allele disrupts the binding site of transcription factor AP-2alpha and expression analysis in the mouse localizes the enhancer activity to craniofacial and limb structures. Our findings place IRF6 and AP-2alpha in the same developmental pathway and identify a high-frequency variant in a regulatory element contributing substantially to a common, complex disorder.
Rahimov
Fedik
F
Department of Pediatrics, University of Iowa, 2182 ML, S Grand Ave, Iowa City, Iowa 52242, USA.
Marazita
Mary L
ML
Visel
Axel
A
Cooper
Margaret E
ME
Hitchler
Michael J
MJ
Rubini
Michele
M
Domann
Frederick E
FE
Govil
Manika
M
Christensen
Kaare
K
Bille
Camille
C
Melbye
Mads
M
Jugessur
Astanand
A
Lie
Rolv T
RT
Wilcox
Allen J
AJ
Fitzpatrick
David R
DR
Green
Eric D
ED
Mossey
Peter A
PA
Little
Julian
J
Steegers-Theunissen
Regine P
RP
Pennacchio
Len A
LA
Schutte
Brian C
BC
Murray
Jeffrey C
JC
D000483:Alleles; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D016022:Case-Control Studies; D002971:Cleft Lip / Q000235:genetics*; D017124:Conserved Sequence; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D020022:Genetic Predisposition to Disease; D006239:Haplotypes; D006801:Humans; D050835:Interferon Regulatory Factors / Q000235:genetics*; D051379:Mice; D008822:Mice, Transgenic; D008969:Molecular Sequence Data; D016017:Odds Ratio; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011485:Protein Binding; D050656:Transcription Factor AP-2 / Q000378:metabolism*
C109803:IRF6 protein, human; C528250:IRF6 protein, mouse; D050835:Interferon Regulatory Factors; D050656:Transcription Factor AP-2