Final Report Summary - FB-REGULOME (The role of gene regulatory elements in forebrain development and epilepsy) Epilepsy is one of the most common neurological disorders, affecting approximately 1-3% of the population and is a significant public health problem. Epilepsy is a spectrum of disorders with a strong genetic component which makes it difficult to precisely diagnose and provide effective treatments. In some cases, erroneous diagnosis of individuals with epilepsy can lead to ineffective drug treatment and/or adverse side effects. Thus, a major challenge is to improve diagnostic tools that can provide better treatment given to individuals with epilepsy.Our long term objectives are to identify gene regulatory elements that are associated with epilepsy and to understand their role in epilepsy pathogenesis. Mutations in gene regulatory elements, such as enhancers, that regulate the spatiotemporal expression of genes could be a major cause of complex disorders such as epilepsy. For example, disruption of these elements and subsequently the gene regulatory networks that they are involved during brain development can lead to early onset epilepsy. Our approach provides a novel dataset of in vivo functional neuronal regulatory elements that control the spatiotemporal expression of epilepsy-associated genes. Using a combination of sequencing based approaches including Chromatin immunoprecipitation followed sequencing (ChIP-seq), chromatin interaction analysis followed pair-end sequencing (ChIA-PET), RNA-seq and functional in vivo assays, we discovered novel epilepsy-associated enhancers and study their mechanism of action. In aim 1, we have identified the genome wide enhancer candidates that could regulate the expression pattern of neuronal genes that expressed in mouse forebrain at embryonic day 16.5. We have focused our effort on studying the regulatory elements of 353 genes that known to be associated with epilepsy and found that there are about 3500 enhancer candidates that could be active in the mouse forebrain. Some of these enhancers shown to physically interact with the promoter regions of their epilepsy associated genes. Furthermore, we analysed the expression patterns of these genes and found that the active enhancers are associated with higher expression of the targeted genes. Thus, our results generated a map of the gene regulatory elements involved in brain development. In aim 2, we have validated our enhancer candidates using in vivo enhancer assay in zebrafish and mouse. We showed that the enhancer marked sequences function as neuronal specific enhancers with similar expression pattern as the targeted genes. In aim 3, we next analyse the DNA motifs of the enhancer sequences that required for in vivo activity and study the potential transcription factors that could activate the enhancers. Combined, this study provides a novel dataset of in vivo functional neuronal regulatory elements that control the spatiotemporal expression of epilepsy-associated genes. Thus, our work will shed light on neuronal gene regulation and regulatory networks involved in epilepsy pathogenesis and brain development. Using this carrier integration grant, I was able to build a research group and expand our knowledge of the involvement of gene regulatory elements in epilepsy and other neurodevelopmental disorders. For example, we are currently working on the regulatory elements of human inhibitory interneurons. As these inhibitory interneurons are know to be associated with early onset epilepsy, we are studying the functional enhancers that might be involved in epilepsy. It allows us not only to identify common neuronal enhancers between human and mouse but also specific enhancers of human inhibitory interneurons. Furthermore, my successful integration in BGU allowed me to collaborate with clinicians and to collect DNA samples from epilepsy patients. These DNA samples are screened for coding and noncoding mutations. For those patients whom no coding mutation could be found, screening for sequencing variants in enhancer candidates could elucidate the molecular mechanism that lead to the patient phenotype. In summary, this grant allowed me to successfully integrate in the scientific community and to establish my own group research. As a result, our work will shed light on neuronal gene regulation and regulatory networks involved in brain development and could pave the way towards future informative dataset for screening noncoding variations in humans with epilepsy and other neurodevelopmental disorders.
