Structural variants disrupt a critical regulatory region downstream of FOXG1

The forkhead box G1 (FOXG1) transcription factor is a crucial regulator during embryonic brain development. Variants affecting the FOXG1 gene result in a congenital form of Rett syndrome, also called FOXG1 syndrome. Interestingly, to date 34 cases with FOXG1-related clinical features have been reported, harboring structural variants (SVs) that disrupt the region downstream of the FOXG1 gene. Yet, the regulatory mechanisms resulting in aberrant FOXG1 transcription have not been elucidated.We identified a non-coding deletion in a patient with FOXG1 syndrome that allowed us to narrow down a ~100kb critical regulatory region affected in all patients with SVs 3’ of FOXG1. By mapping regulatory interactions via UMI-4C, we showed that the FOXG1 promoter interacts with this region during human neuronal development. Using available epigenomics data from human embryonic brain, we found that it contained multiple regulatory elements, including putative brain enhancers, as well as a cluster of CTCF-binding sites forming the distal boundary of the FOXG1-containing topologically associating domain (TAD). Through Hi-C and UMI-4C on patient cells we found that deletion of this region impacts FOXG1 interactions and TAD structure.These results build towards a functional validation of regulatory elements at the FOXG1 locus, crucial for correct SV interpretation.The forkhead box G1 (FOXG1) transcription factor is a crucial regulator during embryonic brain development. Variants affecting the FOXG1 gene result in a congenital form of Rett syndrome, also called FOXG1 syndrome. Interestingly, to date 34 cases with FOXG1-related clinical features have been reported, harboring structural variants (SVs) that disrupt the region downstream of the FOXG1 gene. Yet, the regulatory mechanisms resulting in aberrant FOXG1 transcription have not been elucidated.We identified a non-coding deletion in a patient with FOXG1 syndrome that allowed us to narrow down a ~100kb critical regulatory region affected in all patients with SVs 3’ of FOXG1. By mapping regulatory interactions via UMI-4C, we showed that the FOXG1 promoter interacts with this region during human neuronal development. Using available epigenomics data from human embryonic brain, we found that it contained multiple regulatory elements, including putative brain enhancers, as well as a cluster of CTCF-binding sites forming the distal boundary of the FOXG1-containing topologically associating domain (TAD). Through Hi-C and UMI-4C on patient cells we found that deletion of this region impacts FOXG1 interactions and TAD structure.These results build towards a functional validation of regulatory elements at the FOXG1 locus, crucial for correct SV interpretation.C