Epigenome-wide association study for atrazine induced transgenerational DNA methylation and histone retention sperm epigenetic biomarkers for disease

Abstract

Atrazine is a common agricultural herbicide previously shown to promote epigenetic transgenerational inheritance of disease to subsequent generations. The current study was designed as an epigenome-wide association study (EWAS) to identify transgenerational sperm disease associated differential DNA methylation regions (DMRs) and differential histone retention regions (DHRs). Gestating female F0 generation rats were transiently exposed to atrazine during the period of embryonic gonadal sex determination, and then subsequent F1, F2, and F3 generations obtained in the absence of any continued exposure. The transgenerational F3 generation males were assessed for disease and sperm collected for epigenetic analysis. Pathology was observed in pubertal onset and for testis disease, prostate disease, kidney disease, lean pathology, and multiple disease. For these pathologies, sufficient numbers of individual males with only a single specific disease were identified. The sperm DNA and chromatin were isolated from adult one-year animals with the specific diseases and analyzed for DMRs with methylated DNA immunoprecipitation (MeDIP) sequencing and DHRs with histone chromatin immunoprecipitation (ChIP) sequencing. Transgenerational F3 generation males with or without disease were compared to identify the disease specific epimutation biomarkers. All pathologies were found to have disease specific DMRs and DHRs which were found to predominantly be distinct for each disease. No common DMRs or DHRs were found among all the pathologies. Epimutation gene associations were identified and found to correlate to previously known disease linked genes. This is one of the first observations of potential sperm disease biomarkers for histone retention sites. Although further studies with expanded animal numbers are required, the current study provides evidence the EWAS analysis is effective for the identification of potential pathology epimutation biomarkers for disease susceptibility.

Non-coding RNAs and chromatin: key epigenetic factors from spermatogenesis to transgenerational inheritance

“…In the same line, DHRs position in the genome correlates with genes associated with cell signaling, metabolism and transcription, which may alter zygote and embryo development [ 90 , 91 , 99 ]. Rats exposed to agricultural pesticides showed that DMRs have a positive correlation with DHRs and ncRNAs expression [ 100 ], suggesting both histone retention site guiding by DNA methylation and RNA-directed DNA methylation [ 101 ]. In addition, pericentric histone retention was found to be directed by nuclear RNAs in mature spermatozoa, specifically through the RNA-binding motif of the testis-specific histone variant H2A.L.2 [ 102 ].…”

Predicting environmentally responsive transgenerational differential DNA methylated regions (epimutations) in the genome using a hybrid deep-machine learning approach

“…The goal is to build a classification model that takes a region of the genome as input and predicts the region’s susceptibility to develop an environmentally induced transgenerational alteration in differential DNA methylation regions (DMRs) in the F3 generation from an ancestrally exposed F0 generation (great grandmother). The Skinner laboratory at Washington State University has produced several datasets based on the rat genome that identify DMRs in the F3 generation male sperm after exposing the F0 generation to one of nine toxicants: atrazine [ 15 ], dichloro-diphenyl-trichloroethane (DDT) [ 16 ], glyphosate [ 17 ], vinclozolin [ 18 ], pesticides [ 19 ], dioxin [ 20 ], jet fuel [ 21 ], methoxychlor [ 22 ], and plastics [ 23 ].…”

“…The Skinner laboratory at Washington State University has produced several datasets based on the rat genome that identify the differential DNA methylated regions (DMRs) in the F3 generation after exposure of the F0 generation to one of nine toxicants: atrazine [ 15 ], dichloro-diphenyl-trichloroethane (DDT) [ 16 ], glyphosate [ 17 ], vinclozolin [ 18 ], pesticides permethrin and N,N-Diethyl-meta-toluamide (DEET) [ 19 ], dioxin [ 20 ], jet fuel [ 21 ], methoxychlor [ 22 ], and plastics bisphenol A and phthalates [ 23 ]. Atrazine and glyphosate are commonly used herbicides.…”

Role of epigenetic transgenerational inheritance in generational toxicology

“…Pesticides are environmental toxicants and induce the transgenerational inheritance of increased disease risk, ( Table 1 ). Ancestral exposure of pregnant rats to the herbicide atrazine induced transgenerational increases in testis disease, prostate disease, kidney disease, a lean phenotype, and an altered age at puberty [ 64 , 65 ]. DDT exposure increases obesity transgenerationally but also induces increased rates of testis, ovary, and kidney pathologies [ 61 ].…”