Noncoding structural variants disrupt the regulatory architecture of Rett genes

Rett syndrome is a progressive neurodevelopmental disorder, characterized by a severe developmental delay, absence of speech, seizures, hypotonia and stereotypic movements. It is typically caused by mutations in the MECP2 gene, but several other genes, including the transcription factors MEF2C and FOXG1, have been associated with a Rett-like phenotype as well. Recently, we and others identified several noncoding structural variants (SVs) in patients with Rett-like characteristics. All SVs are located proximal to the coding sequence of MEF2C or FOXG1, suggesting disruption of the regulatory structure governing these genes. Using Circularized Chromosome Conformation Capture (4C) sequencing in a neuronal cell line, we identified a complex regulatory interaction network in the MEF2C region. We found that the MEF2C promoter physically contacts multiple distal enhancer regions upstream of its coding sequence. Based on epigenetic enhancer marks and sequence conservation, we delineated 16 putative enhancer elements, of which 14 were active in in vitro luciferase assays and 8 displayed in vivo neuronal activity during zebrafish development. For FOXG1 as well, 4C-seq experiments have shown that the promoter interacts with at least three in vivo validated brain enhancers, all situated in a region affected by deletions or translocations in multiple Rett-like patients. In summary, Rett genes MEF2C and FOXG1 are part of complex regulatory networks involving multiple distal enhancers. Disruption of these regulatory structures by noncoding SVs could form the genetic basis of the Rett-like phenotype observed in some patients.