Deletion of FOXG1 transcriptional enhancers is associated with Rett-like syndrome

Gene regulatory elements such as enhancers dynamically regulate gene expression in a tissue-specific manner. However, the transcriptional regulatory elements during human inhibitory interneuron differentiation and their role in neurodevelopmental disorders are unknown. Here, we generated gene regulatory element maps of human inhibitory-like interneurons derived from embryonic stem cells (H9-ESC), permitting large-scale annotation of previously uncharacterized regulatory elements relevant to inhibitory interneuron differentiation. Our analyses identify neuronal progenitor enhancers that likely regulate the expression of transcription factors that are essential for interneuron differentiation. One of these transcription factors is FOXG1 that is specifically expressed in interneuron progenitors. Haploinsufficiency of FOXG1, is associated with Rett-like syndrome. Using in vivo enhancer assay, we identified eight transcriptional enhancers in the FOXG1 locus with activity patterns that resembled FOXG1 expression. Using CRISPR/Cas9 genome editing, we deleted two FOXG1 enhancers which reduced FOXG1 expression in human U251 cells and altered cell proliferation. Furthermore, a microdeletion proximal to FOXG1 encompassing these neuronal FOXG1 enhancers was found in patient with Rett-like syndrome, supporting the role of FOXG1 enhancers in this syndrome. Our study provides a framework for understanding the impact of non-coding regulatory elements during inhibitory interneuron differentiation, and highlights novel mechanisms underlying neurodevelopmental disorders