The dysmorphology and phenotype were tested in the whole embryo culture model for alcohol-induced abnormalities with distinct sub-phenotypes related to timely neural tube closure. Described as neural tube closed (NTC), neural tube opened (NTO);65 the heat map of the gene distribution of these two sub-phenotypes are also found sub-clustered (Manuscript in preparation; gene expression profile uploaded in GEO Accession# GSE9545); thus, DNA methylation levels in these two sub-phenotypes were further observed. We mapped the promoter methylome at the early neurulation stage of the embryonic development using a high-throughput analysis, “MeDIP” (methylated DNA immunoprecipitation), coupled with microarray analysis for genome-wide identification of hyper- and hypo-methylation of genes.54 DNA methylation was analyzed mainly at 1.8 Kb promoter regions around transcription start sites (www.nimblegen.com, Madison, WI); validation of the MeDIP results was confirmed by Sequenom Mass ARRAY of target genes.
