FOXG1 mutations alter the 3D chromatin structure in the context of microcephaly and neuronal function

• Applicant: Professorin Dr. Tanja Vogel
• Subject Area: Developmental Neurobiology
• Term: since 2026
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 573347294

Developmental programs that orchestrate proper specification of neuronal networks are genetically determined. Disturbance of these tightly regulated programs can be the neurodevelopmental basis of cognitive diseases, including microcephaly. By definition, microcephaly refers to a smaller brain and head circumference. Primary microcephaly is a human neurodevelopmental disorder (NDD), that is caused by a disbalance of cortical neural stem cell (NSC) proliferation and differentiation. The transcription factor FOXG1 confounds upon mutation a severe and rare NDD, named FOXG1-syndrome (OMIM #613454). Different types of dominant mutations in the human FOXG1 gene have been identified, and microcephaly is conspicuous among variable clinical features. FOXG1 is one key regulator of forebrain development with intricate expression dynamics. In mice, high FOXG1 levels maintain the self-renewal of the NSC pool. Transient downregulation initiates neurogenesis, but maturing neurons regain FOXG1 expression for subtype specification, migration and integration into functional neuronal networks. We have indication that human FOXG1 mRNA expression dynamics recapitulates this dynamics in brain organoids derived from human induced pluripotent stem cells (iPSC), but that FOXG1 mutations disturb the dynamics compared to healthy donor (HD) control organoids. Different FOXG1 mutations correlate with different expression dynamics. Further, our preliminary data suggest functional synergies of FOXG1 and proteins impacting the chromatin architecture. Therefore, we propose this project with its main objective to advance understanding of the emerging topological aspect of transcriptional regulation of and by FOXG1. Using iPSC-derived NSCs, we aim (i) to enlighten global changes of chromatin binding for FOXG1, and interacting chromatin modifiers in the context of the FOXG1 c.765G>A nonsense mutation, (ii) to determine binding of FOXG1, and chromatin modifiers at the FOXG1 gene locus to understand whether these protein complexes impact FOXG1's transcriptional regulation, and (iii) to decipher the 3D layout at the FOXG1 gene by characterising predicted chromatin loops upon FOXG1 mutation. Since we observed RNA-dependence for many interactions of FOXG1 with chromatin modifiers, our study also aims to highlight the nature of RNAs impacting different FOXG1 functions. Finally, to advance mechanistic understanding of how human FOXG1 regulates early brain development we will study human brain organoids as more realistic model system compared to NSCs. Brain organoids will derive from iPSC with or without FOXG1 mutations, and we will enrich specific cell types using FACS to assess whether and which cell types exhibit altered FOXG1 expression dynamics. We will determine whether the regulative mechanisms impacting the chromatin architecture in NSCs confer dynamic FOXG1 expression in brain organoids as well.

• DFG Programme: Research Grants