Genome-wide DNA methylation analysis reveals phytoestrogen modification of promoter methylation patterns during embryonic stem cell differentiation

• Published in: PloS one 2011-04, Vol.6 (4), p.e19278-e19278
• Main Authors: Sato, Noriko, Yamakawa, Naomi, Masuda, Moe, Sudo, Katsuko, Hatada, Izuho, Muramatsu, Masaaki
• Format: Article
• Language: English
• Subjects: Adipocytes; Analysis; Animals; Biology; Biosynthesis; Bisphenol A; Cell differentiation; Cell Differentiation - drug effects; Chemistry; CpG Islands; Critical period; Deoxyribonucleic acid; Differentiation (biology); DNA; DNA - genetics; DNA Methylation; DNA microarrays; Embryogenesis; Embryonic growth stage; Embryonic stem cells; Embryonic Stem Cells - cytology; Endonuclease; Environment; Epidemiology; Epigenesis, Genetic; Epigenetic inheritance; Epigenetics; Fetuses; Gene expression; Gene regulation; Genes; Genetic testing; Genistein; Genistein - pharmacology; Genome; Genomes; Genomics; Geriatrics; Glycine max; Implantation; Isoflavones; Leukemia; Medical research; Medicine; Methylation; Mice; Mice, Inbred C57BL; Mitochondrial DNA; Phytoestrogens - metabolism; Promoter Regions, Genetic; Proteins; Reverse Transcriptase Polymerase Chain Reaction; Science; Stem cells
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0019278

Environmental challenges during development affect the fetal epigenome, but the period(s) vulnerable to epigenetic dysregulation is(are) not clear. By employing a soy phytoestrogen, genistein, that is known to alter the epigenetic states of the A(vy) allele during embryogenesis, we have explored the sensitive period for epigenetic regulation. The post-implantation period, when de novo DNA methylation actively proceeds, is amenable to in vitro analysis using a mouse embryonic stem (ES) cell differentiation system. Mouse ES cells were differentiated in the presence or absence of genistein, and DNA methylation patterns on day 10 were compared by microarray-based promoter methylation analysis coupled with a methylation-sensitive endonuclease (HpaII/McrBC)-dependent enrichment procedure. Moderate changes in methylation levels were observed in a subset of promoters following genistein treatment. Detailed investigation of the Ucp1 and Sytl1 promoters further revealed that genistein does not affect de novo methylation occurring between day 0 and day 4, but interferes with subsequent regulatory processes and leads to a decrease in methylation level for both promoters. Genistein perturbed the methylation pattern of differentiated ES cells after de novo methylation. Our observations suggest that, for a subset of genes, regulation after de novo DNA methylation in the early embryo may be sensitive to genistein.