Molecular interactome of HNRNPU reveals regulatory networks in neuronal differentiation and DNA methylation

HNRNPU is an RNA-binding protein with diverse roles in regulating gene expression. Pathogenic genetic variants of HNRNPU cause a severe neurodevelopmental disorder (NDD), but the underlying molecular mechanisms are unclear. Here, we investigated the protein-protein interaction (PPI) network and RNA targets of HNRNPU in neuroepithelial stem cells (NES) and differentiating neural cells derived from human induced pluripotent stem cells. Using high-throughput approaches, we found HNRNPU interacting with the mammalian SWI/SNF complex and highlight its putative role in multiple stages of mRNA regulation. Notably, both PPI partners and interacting mRNAs implicated HNRNPU in translation, a role that had not been recognized before. Also, we found that HNRNPU associated with mRNAs encoding proteins important for neuronal development. Based on our findings, we propose a regulatory model in which HNRNPU, in coordination with SWI/SNF, modulates the levels and accessibility of DNA methylation factors, leading to global methylation differences in HNRNPU deficiency states, as we validated in our cell model. This mechanism provides a molecular link to the distinct methylation signature seen in individuals with HNRNPU-related NDDs as well as to crucial epigenetic regulation during early brain development.