A candidate HNRNPU-CHD2 RNA-processing axis in neurodevelopmental disease

Abstract

Heterozygous loss-of-function variants in HNRNPU, which encodes a nuclear RNA-binding scaffold protein, cause a neurodevelopmental disorder with epilepsy, intellectual disability and brain malformations, but the programs that link HNRNPU dosage to neuronal dysfunction remain poorly defined. We depleted HNRNPU in Human embryonic kidney 293T (HEK293T) cells, profiled gene expression and alternative splicing, intersected the two datasets, and asked which of the resulting genes already carried a neurodevelopmental annotation. Knockdown produced 5,643 differentially expressed genes and 21,728 high-confidence splicing events; 1,222 genes changed at both levels, and two pre-specified neurodevelopmental panel genes were among them: CHD2 and DYRK1A. In K562 eCLIP experiments, 107 reproducible HNRNPU peaks were detected across the CHD2 gene body, and three of the four regulated exons introduce a reading-frame shift whose premature termination codon lies far upstream of the final exon junction, predicting nonsense-mediated decay. Public K562 knockdown data reproduced the rise in CHD2 mRNA and the same skipped-exon change, and CHD2 depletion in the neural line SH-SY5Y altered cell-cycle, DNA-repair and neural gene programs. HNRNPU therefore constrains a frameshift-prone splicing switch in CHD2, a candidate route from HNRNPU haploinsufficiency to loss of functional CHD2 if these transcripts are degraded.