Structural variants in the Epb41l4a locus: TAD disruption and Nrep gene misregulation as hypothetical drivers of neurodevelopmental outcomes

Abstract

Structural variations are a pervasive feature of human genomes, and there is growing recognition of their role in disease development through their impact on spatial chromatin architecture. This understanding has led us to investigate the clinical significance of CNVs in noncoding regions that influence TAD structures. In this study, we focused on the Epb41l4a locus, which contains a highly conserved TAD boundary present in both human chromosome 5 and mouse chromosome 18, and its association with neurodevelopmental phenotypes. Analysis of human data from the DECIPHER database indicates that CNVs within this locus, including both deletions and duplications, are often observed alongside neurological abnormalities, such as dyslexia and intellectual disability, although there is not enough evidence of a direct correlation or causative relationship. To investigate these possible associations, we generated mouse models with deletion and inversion mutations at this locus and carried out RNA-seq analysis to elucidate gene expression changes. We found that modifications in the Epb41l4a TAD boundary led to dysregulation of the Nrep gene, which plays a crucial role in nervous system development. These findings underscore the potential pathogenicity of these CNVs and highlight the crucial role of spatial genome architecture in gene expression regulation.

Figure 1

(A) Hi-C profile around human EPB41L4A locus and locations of protein coding genes. (B) Coordinates of DECIPHER patient’s CNVs. Blue—duplications, red—deletions. (C) ChIP-Seq profiles of CTCF binding and H3K27ac and H3K4me1 histone marks of human EPB41L4A locus. (D) Coordinates of mouse lines mutations. Red—deletion of DNA fragment, green—inversion. (E) Hi-C profile around murine Epb41l4a locus and locations of protein coding genes.

Figure 2

(A) Scheme of enhancer hijacking mechanism in the inversion model. Green circle represents Nrep enhancer, scissors—CRISPR/Cas9 targets. (B) Expression changes of Nrep and Epb41l4a in cerebellum for inversion model. (C) Nrep expression in cerebellum for deletion model, (D) Nrep expression in cerebellum for inversion model, (E) Epb41l4a expression in olfactory bulb for deletion model, (F) Epb41l4a expression in cerebellum for deletion model. WT—expression level of wild-type mice, INV—for mice carrying inversion. Y-scale of gene expression bar plots represents DeSeq2 normalized counts.