A statistical approach to identifying significant transgenerational methylation changes

Epigenetic aberrations have profound effects on phenotypic output. Genome-wide methylation alterations are inheritable to pass down the aberrations through multiple generations. We developed a statistical method, Genome-wide Identification of Significant Aberration in Methylation, GISAIM, to study the significant transgenerational methylation changes. GISAIM finds the significant methylation aberrations that are inherited through multiple generations. In a concrete biological study, we investigated whether exposing pregnant rats (F0) to a high fat (HF) diet throughout pregnancy or ethinyl-estradiol (EE2)-supplemented diet during gestation days 14–20 affects carcinogen-induced mammary cancer risk in daughters (Fl), granddaughters (F2) and great-granddaughters (F3). Mammary tumorigenesis was higher in daughters and granddaughters of HF rat dams, and in daughters, granddaughters and great-granddaughters of EE2 rat dams. Outcross experiments showed that increased mammary cancer risk was transmitted to HF granddaughters equally through the female or male germlines, but is only transmitted to EE2 granddaughters through the female germline. Transgenerational effect on mammary cancer risk was associated with increased expression of DNA methyltransferases, and across all three EE2 generations hypo-or hyper-methylation of the same 375 gene promoter regions in their mammary glands. Our study shows that maternal dietary estrogenic exposures during pregnancy can increase breast cancer risk in multiple generations of offspring, and the increase in risk may be inherited through non-genetic means, possibly involving DNA methylation.