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.
Department of Pediatrics, University of Iowa, 2182 ML, S Grand Ave, Iowa City, Iowa 52242, USA.
Fedik
F
Rahimov
Mary L
ML
Marazita
Axel
A
Visel
Margaret E
ME
Cooper
Michael J
MJ
Hitchler
Michele
M
Rubini
Frederick E
FE
Domann
Manika
M
Govil
Kaare
K
Christensen
Camille
C
Bille
Mads
M
Melbye
Astanand
A
Jugessur
Rolv T
RT
Lie
Allen J
AJ
Wilcox
David R
DR
Fitzpatrick
Eric D
ED
Green
Peter A
PA
Mossey
Julian
J
Little
Regine P
RP
Steegers-Theunissen
Len A
LA
Pennacchio
Brian C
BC
Schutte
Jeffrey C
JC
Murray
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