Evaluation of chromatin accessibility in cultured fetal hypothalamic neuroprogenitors following maternal protein restriction in rats.

Maternal protein restriction (PR) is a risk factor for altered fetal neurodevelopment and increased susceptibility to neurometabolic disorders later in life. Although structural and transcriptomic changes in the developing hypothalamus have been reported in PR-exposed offspring, the underlying regulatory mechanisms remain unclear. We hypothesized that maternal PR alters chromatin accessibility in hypothalamic neuroprogenitor cells, potentially disrupting gene regulation critical for cell fate specification. We performed ATAC-seq on hypothalamic neuroprogenitors isolated at gestational day 17 from rat fetuses that were exposed to an isocaloric PR diet. We identified 312 chromatin regions with different accessibility, including regions with reduced accessibility near genes encoding Major Histocompatibility Complex class I (MHC-I) proteins, amino acid transporters and proteins involved in neuronal differentiation, and synaptic signaling. Motif enrichment analysis revealed reduced accessibility at FOS/JUN and DBP binding sites in PR samples, alongside enrichment of Krüppel-like transcription factor motifs in more accessible regions. RNA-seq on neurospheres generated from these progenitors identified 91 candidate genes with altered expression patterns, enriched in pathways related to cell proliferation, protein-lipid metabolism, and apoptosis. Integration with previously generated single-cell RNA-seq data associated several of these genes with specific neuroprogenitor subpopulations. Except for two genes (RT1-A2 and Nav2), differences in chromatin accessibility were not associated with significant changes in neighboring gene expression. These findings provide an initial resource for exploring chromatin regulation in fetal rat hypothalamic progenitors. They suggest that maternal PR may influence developmental trajectories by altering chromatin accessibility and, consequently, be a mechanism underlying fetal programming of metabolic dysfunction.