PUTATIVE REGULATORY ROLES OF LONG NON‑CODING RNAS FROM THE HNRNPU LOCUS DURING NEURAL DEVELOPMENT

Deletions and point mutations affecting the HNRNPU locus at chr1q44 cause HNRNPU‑related neurodevelopmental disorder (HNRNPU‑NDD). The locus comprises the protein‑coding HNRNPU gene and ten long non‑coding RNAs (lnc‑HNRNPUs), yet the contribution of locus‑wide deletions in comparison to point mutations affecting HNRNPU alone remains unclear.
HNRNPU encodes an RNA‑ and DNA‑binding protein with essential roles in 3D-genome architecture, transcription, RNA stability, and alternative splicing. We recently expanded its molecular characterization by defining the HNRNPU protein interactome, RNA targets, and effects on global DNA methylation. However, whether different genetic variations at the HNRNPU locus result in distinct molecular and developmental consequences remains unexplored.
Here, we investigate whether deletions spanning both HNRNPU and lnc‑HNRNPUs differ from mutations confined to HNRNPU and assess the role of lnc‑HNRNPUs in early neurodevelopment. We used six different induced pluripotent stem cell lines, including a patient with HNRNPU-NDD carrying a 44 kb heterozygous deletion spanning the HNRNPU locus, two isogenic CRISPR‑Cas9 mutant lines recapitulating the deletion and indels resulting in an early stop codon in HNRNPU. The iPSCs were differentiated into neuroepithelial stem cells and early cortical organoids.
Genome‑wide methylation profiling revealed opposite epigenomic signatures between full‑locus deletions and HNRNPU‑only mutations. Furthermore, RNA immunoprecipitation sequencing identified direct interactions between HNRNPU and lnc‑HNRNPUs. Silencing of these lncRNAs reduced HNRNPU protein levels, suggesting a regulatory feedback mechanism within the locus. Current work focuses on analyzing the expression patterns of the lnc-HNRNPUs, clarifying their functions during neurodevelopment.