Biology subjects

Zografidou, L.

Publications and source records attributed to Zografidou, L..

2 recordsLinked to original sources

bioRxiv2026

16p11.2 Copy Number Variation Alters Genome Architecture and Transcriptional Regulation During Neurodevelopment

Microdeletions and microduplications in 16p11.2 are responsible for a spectrum of neurodevelopmental disorders (NDDs) with partially reciprocal and overlapping symptoms. However, the clinical variability in 16p11.2 microduplication patients is significantly greater than that in patients carrying a microdeletion. Here, we use iPSCs derived from members of a family carrying a 16p11.2 microduplication and model neurodevelopment through in vitro differentiation into neural progenitor cells (NPCs) and neurons. The analysis is complemented by reanalysis of publicly available data from 16p11.2 microdeletion patients. Transcriptome analysis revealed MAPK3-centered hubs of upregulated genes in the microduplication-carrying and downregulated in the microdeletion-carrying cells, indicating that MAPK3 is a central driver of 16p11.2 Copy Number Variation (CNV) pathology. While genes within the 16p11.2 region showed about a two-fold reduction in expression in cells carrying the microdeletion, their expression levels in microduplication-derived NPCs and neurons, but not in iPSCs, were elevated to a degree much higher than expected. This observation was accompanied by a substantial number of dysregulated genes unrelated to the genes in the critical region or their interaction networks. To further investigate whether altered chromatin organization may accompany these transcriptional changes, we generated Hi-C data from patient and control iPSCs and NPCs. This revealed increased chromatin contacts within the duplicated 16p11.2 region in patient-derived iPSCs, while genome-wide compartment analysis showed that increased compartments preferentially co-occurred with upregulated differentially expressed genes, particularly in NPCs. Together, these findings suggest that 16p11.2 microduplication may influence gene expression through both local dosage-dependent mechanisms and broader, differentiation-associated changes in chromatin organization. Our data support a model in which CNV-associated genome architecture changes may modulate transcriptional dysregulation and contribute to the variable neurodevelopmental phenotypes associated with 16p11.2 rearrangements.

pathology↗

bioRxiv2024

Premature upregulation of miR-92a's target RBFOX2 hijacks PTBP splicing and impairs cortical neuronal differentiation.

Alternative splicing is a crucial component of neuronal differentiation, yet the mechanisms that regulate splicing transitions during embryonic brain development remain incompletely understood. Here, we identify a post-transcriptional mechanism that times the expression of the splicing factor Rbfox2 during neurogenesis. RBFOX2 is normally expressed at low levels in neural progenitor cells (NPCs) and becomes upregulated in newborn neurons where it promotes neuronal differentiation. Unexpectedly, premature expression of Rbfox2 in NPCs of the embryonic mouse neocortex blocked their differentiation into neurons rather than promoting it. Genome-wide analysis revealed widespread alternative splicing changes enriched for NDD genes and associated with a hybrid NPC- and neuron-like splicing pattern that significantly deviates from the normal splicing developmental trajectory. Remarkably, premature Rbfox2 expression induced the inclusion of validated target exons that are otherwise repressed by PTBP2 pointing to an antagonistic splicing relationship. Integrative scRNA-seq analysis confirmed a negatively correlated expression between these two RNA-binding proteins (RBP) along differentiation pseudotime. Strikingly, we identified the NPC-specific miRNA 92a-3p as a regulator of the Rbfox2 expression switch: expression of miR-92a reduced RBFOX2 levels and reversed splicing patterns of target genes in vitro, while silencing miR-92a in vivo increased RBFOX2 expression in the embryonic cortex. Together, these findings reveal a previously unrecognized miRNA-RBP regulatory axis that ensures the proper timing of NPC-to-neuron splicing transitions in the developing cortex and provide new insights into splicing dysregulation as a contributing factor to the emergence of neurodevelopmental disorders. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=152 HEIGHT=200 SRC="FIGDIR/small/614071v3_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@16248caorg.highwire.dtl.DTLVardef@198dd0dorg.highwire.dtl.DTLVardef@d8887aorg.highwire.dtl.DTLVardef@1e8419e_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical Abstract Schematic representation of the proposed splicing regulation for the transition of undifferentiated NPCs to neurons in the developing cerebral cortex.

genomics↗