Heterochronic regulation of neural development

Congenital hydrocephalus (CH) involves ventricular enlargement and has historically been attributed to impaired cerebrospinal fluid (CSF) flow. Recent evidence, however, reveals that neurodevelopmental defects underlie many CH cases. Indeed, genetic studies frequently implicate neural differentiation and timing factors rather than direct regulators of CSF homeostasis. Our work focuses on the MIR302 family of microRNAs, which orchestrate developmental timing by controlling both post-transcriptional and epigenetic programs. We previously found that complete loss of mir-302 causes severe neural tube defects. More recently, we developed a hypomorphic mir- 302 mouse model that displays classic CH features—dome-shaped skulls, ventriculomegaly, and aqueduct stenosis—and exhibits altered chromatin accessibility in neural stem cells. Preliminary single-nuclei RNA- sequencing indicates a defect in neurogenesis across forebrain and midbrain populations, highlighting a broader timing dysregulation. We hypothesize that miR-302 enforces heterochronic control of neuroepithelial stem cells, preventing precocious differentiation and safeguarding specialized structures like the subcommissural organ (SCO). In Aim 1, we will define how miR-302 functions as a post-transcriptional regulator by mapping direct miRNA:mRNA interactions (via AGO2-chimeric eCLIP) and measuring translational changes (via Ribo-seq), thus linking aberrant gene expression to the loss of miR-302. In Aim 2, we will examine how distinct MIR302 members modulate chromatin accessibility, particularly in dorsal midbrain cells forming the SCO, using single-nuclei RNA+ATAC multiome and Polycomb (PRC2) occupancy assays. By pinpointing the epigenetic mechanisms that fail in CH mutants, we will reveal why the SCO is especially susceptible to timing defects. Together, these studies will yield new insights into how miRNA-driven heterochronic regulation ensures proper neuronal lineage commitment and SCO maintenance—key processes disrupted in CH. Our findings may inform novel therapeutic strategies aimed at restoring developmental timing in congenital brain malformations. Project Number: 1R01HD118492-01A1 | Fiscal Year: 2026 | NIH Institute/Center: Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) | Principal Investigator: Ronald Parchem | Institution: BAYLOR COLLEGE OF MEDICINE, HOUSTON, TX | Award Amount: $601,082 | Activity Code: R01 | Study Section: Developmental Brain Disorders Study Section[DBD] View on NIH RePORTER: https://reporter.nih.gov/project-details/11298318