Epigenetic Regulation of Serine Biosynthesis by PHF8 During Neurogenesis [ChIP-Seq H3K9me3]

During neurodevelopment, progenitor proliferation is a highly orchestrated process, involving precise epigenetic modifications and immense metabolic demands. Yet, the intricate interplay between epigenetics and metabolism remains largely unexplored. To investigate this, we utilized neural stem cells to examine the role of PHF8, a histone demethylase whose mutations are linked to Siderius-Hamel syndrome, a rare neurodevelopmental disorder. Through an integrated multi- omics approach—combining transcriptomics, epigenomics, and metabolomics—we identify PHF8 as a key driver of the serine biosynthesis pathway, safeguarding the intracellular serine pool essential for neural progenitor proliferation. PHF8 fine- tunes chromatin accessibility at promoters of metabolic genes, ensuring their activation during development. Notably, loss of PHF8 not only disrupts amino acid metabolism and mTORC1 signaling, but also blocks autophagic flux, and impairs vesicle formation—ultimately stalling proliferation and triggering replicative defects and DNA damage. In vivo, PHF8 deficiency in mouse embryos halts neurogenesis, affecting progenitor expansion and neuron generation in the developing brain. Altogether, our work positions PHF8 as a pivotal molecular node linking chromatin dynamics, metabolic regulation, and neural development. These findings not only deepen our understanding of brain development but also open new avenues for exploring the epigenetic basis of metabolic and neurodevelopmental disorders. Overall design: 1x 10^6 shCTR and shPHF8 NSCs were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator. The libraries were prepared and amplified to make DNA NanoBall (DNB) Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)