Fig. 1

Fetal-neonatal ID and prenatal choline supplementation altered chromatin accessibility landscape in P65 FID rat hippocampus. A ATAC-seq data showing differentially-accessible sites and associated genes between treatment groups. Numbers of differential sites include gene bodies, promoter regions (proximal, + 1 K, + 3 K), and intergenic regions. Selection criteria were absolute log2(Fold Change) > 0.2 and false discovery rate q-value < 0.05, n = 4/group. B Distribution of sites with differential accessibility. (C, D) Ingenuity Pathway Analysis (IPA) mapped loci with differential ATAC peaks (within gene bodies or promoter regions) onto biofunctions (C) and canonical signaling pathways (D), ranked hierarchically. Comparisons were made among formerly iron-deficient (FID), formerly iron-deficient with choline (FIDch), and iron-sufficient with choline (ISch) normalized by the iron-sufficient (IS) control group. Squares with dots have absolute z-scores < 2.0, indicating non-significant findings. Blue and orange colors indicate decreased and increased chromatin accessibilities, respectively. Fewer changes were found in the FID compared to FIDch and ISch groups (absolute z-scores > 2.0). Choline induced both decreased and increased chromatin accessibility in the FIDch and ISch groups. E Venn diagram showing overlap and non-overlapping genes modified in FID and FIDch groups. +/−/n indicates increased, decreased, and normalized changes in ATAC signatures. Blue and orange indicate decreased and increased ATAC signatures, respectively. F Comparison between ISch and IS control group showing the choline effect on ATAC landscape in adult rat hippocampus. IPA generates a graphical summary showing decreased accessibility in loci regulating hippocampal and cortical development centered on microtubule dynamics and canonical pathways showing both increased and decreased ATAC signatures