Integrated analysis of methylomic and transcriptomic profiles in fetal mouse hypothalamus in response to maternal gestational exposure to arsenic.

Background: Gestational exposure to arsenic poses significant risks to fetal development by crossing the placental barrier and disrupting key physiological systems. Although animal studies suggest arsenic impairs hypothalamic development and neuroendocrine function, the precise molecular mechanisms remain poorly understood.

Methods: Pregnant ICR mice were divided into control and arsenic-exposed groups, with the exposed group receiving 4 mg/L of As₂O₃ in deionized water during gestation. Offspring were euthanized on postnatal day 21, and hypothalamic tissues were collected for molecular analysis. Whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq) were performed to identify differentially methylated regions (DMRs), differentially methylated region-associated genes (DMGs), and differentially expressed genes (DEGs). Functional annotation was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, and RNA-seq findings were validated using quantitative real-time PCR (RT-qPCR).

Results: The DNA methylation analysis uncovered widespread changes in response to arsenic exposure, resulting in both hypermethylated and hypomethylated regions. These alterations were predominantly observed in CG and CHH contexts and were notably enriched in crucial genomic regions such as promoters, exons, introns, and repeat regions. Overall, 14,587 DMRs were detected, with 7567 regions exhibiting hypermethylation and 7020 regions displaying hypomethylation. Subsequent RNA-seq analysis identified 373 DEGs linked to pathways involving cytokine interactions, neuroactive ligands, and antigen presentation. Additionally, RT-qPCR results for genes selected from the enriched cytokine-cytokine receptor interaction pathway, as well as eight randomly chosen genes, consistently validated the findings from the RNA-Seq data. Integrated analysis revealed that genes with hypermethylated promoters tended to be downregulated, while those with hypomethylated promoters were often upregulated, supporting a regulatory association between DNA methylation and gene expression.

Conclusion: This integrative analysis of methylomic and transcriptomic profiles in fetal mouse hypothalamus provides insights into the epigenetic and transcriptional responses to gestational arsenic exposure.