ATAC and histone H3K9me3 landscapes revealed the altered epigenome by fetal-neonatal iron deficiency in the adult male rat hippocampus

Iron deficiency during the fetal-neonatal period results in long-term neurodevelopmental impairments associated with pervasive and widespread hippocampal gene dysregulation. Globally, fetal-neonatal iron deficiency produces both long-term activation and repression of hundreds of loci in the adult rat hippocampus. Prenatal choline (a methyl donor) supplementation can partially reverse these effects, suggesting an interaction between iron and choline in regulating the hippocampal transcriptome. To gain insights into the underlying epigenetic signatures, we integrate hippocampal transcriptomes and epigenetic marks of active (transposase accessible chromatin/ATAC) and repressed (H3K9me3 enrichment) genes in adult rats that had been exposed to fetal-neonatal iron deficiency with or without prenatal choline supplementation. Rats were made iron-deficient during fetal and neonatal period by limiting maternal iron intake from gestational day (G) 2 through postnatal day (P) 7. Choline (5.5 g/kg) was given to half of the pregnant dams during G11-18. This paradigm produced four comparison groups (Iron-sufficient [IS], Iron-deficient [ID], IS+choline [ISch], and ID+choline [IDch]). Hippocampi were collected from P65 males and analyzed for changes in chromatin conformation and histone H3K9me3 enrichment. ATAC-seq results accounted for 22% and 24%, whereas H3K9me3 enrichment accounted for 1.7% and 13% of differences in ID- and IDch-altered gene expression. These epigenetic changes were annotated onto gene networks regulating synaptic structure and plasticity, neuroinflammation, and reward circuits. The low correlation between gene dysregulation and changes in ATAC or H3K9me3 signatures indicate involvements of other epigenetic modifications. This study provides a genome-wide findings of stable epigenetic changes and lays a foundation for further analyses to elucidate more fully iron-dependent epigenetic mechanisms that underlie iron deficiency, choline supplementation, and their interactions in mediating long-term neural gene dysregulation. SIGNIFICANCE STATEMENTEarly-life iron deficiency can lead to long-term neurocognitive dysfunction and persistent neural gene dysregulation, despite prompt iron replenishment, suggesting that iron deficiency results in long-term neuroepigenomic changes. This study combined RNA-seq, ATAC-seq, and ChIP-seq to provide the epigenetic basis for gene dysregulation due to fetal-neonatal iron deficiency and prenatal choline supplementation. We found that early-life iron deficiency alters epigenetic regulation of genes involved in neuronal development, cell signaling, neuroinflammation, and reward-related cognition. While choline supplementation to iron-deficient animals partially reverses these effects, it also leads to dysregulation of genes in iron-sufficient animals. The patterns of gene dysregulation were positively correlated with differences in chromatin accessibility and negatively correlated with repressive histone H3K9me3 modification. Our results indicate that these changes at the epigenetic level partially account for the long-term hippocampal gene dysregulation.