Investigations of the genomic region that contains the clf1 mutation, a causal gene in multifactorial cleft lip and palate in mice

Abstract BACKGROUND Human nonsyndromic cleft lip and palate, CL(P), is genetically complex, with one contributing gene on chromosome 17q. A potentially homologous gene, clf1 on distal chromosome 11, is part of the digenic cause of the 10–30% CL(P) in the A/WySn mouse strain. Here we report our progress toward identifying the clf1 mutation. METHODS Transcription from all of the known and predicted genes in the 1.5‐Mb candidate region was examined in A/WySn and control (AXB‐4/Pgn) ED10–11 embryo heads. The marker haplotype for 28 inbred strains across the clf1 region was obtained. The entire transcripts of Wnt9b and Wnt3 in A/WySn were sequenced. Using long PCR, the genomic region from Wnt3 through Wnt9b was screened in A/WySn for an inserted retrotransposon. RESULTS Gosr2 , Wnt9b , Wnt3 , Nsf , Arf2 , Crhr1 , Mapt , Cdc27 , Myl4 , Itgb3 , chr11 _ 20.152 , chr11 _ 20.154 , chr11 _ 20.155 , and chr11 _ 20.15 6 are expressed in ED10–11 heads. None is absent or detectably reduced in A/WySn. The ancestral pre‐ clf1 mutation haplotype was found in CBA/J mice. By a test‐cross, CBA/J was confirmed to lack the clf1 mutation. Three single‐nucleotide variants in A/WySn (vs. C57BL/6J) were found in each of the 3′ untranslated regions (3′UTRs) of Wnt3 and of Wnt9b , respectively; their presence in CBA/J shows that none are the clf1 mutation. An inserted intracisternal A particle (IAP) retrotransposon located 6.6 kb from the 3′ end of Wnt9b was found in A/WySn and in all clf1 strains tested. This IAP is absent in C57BL/6J and CBA/J. CONCLUSIONS The clf1 mutation is a genomic alteration present in A/WySn and absent in the ancestral chromosomal segment in CBA/J. The IAP retrotransposon insertion near Wnt9b in A/WySn fits this criterion; we predict that interference with Wnt9b function by this IAP is the clf1 mutation. Birth Defects Research (Part A) 2005. © 2005 Wiley‐Liss, Inc.