GSE96915
The Psychiatric Risk Gene Transcription Factor 4 (TCF4) Regulates Neurodevelopmental Pathways Associated With Schizophrenia, Autism, and Intellectual Disability
Common genetic variants in and around the gene encoding transcription factor 4 (TCF4) are associated with an increased risk of schizophrenia whereas rare variants have been found in patients with intellectual disability (ID), developmental disorders and autism spectrum disorder (ASD). Haploinsufficiency of TCF4 also causes Pitt Hopkins syndrome (PTHS); a condition characterized by developmental delay, ID and autonomic dysfunction. To understand the role of TCF4 in these disorders, we have used chromatin immunoprecipitation and next generation sequencing (ChIP-seq) to identify the genomic binding sites for TCF4. In this study we identify 10,604 binding sites assigned to 5,437 genes. De novo motif enrichment found that approximately 77% of the TCF4 binding sites contained at least one E-box (5'-CAtcTG). Furthermore, the majority of TCF4 binding sites overlapped with H3K27ac histone mark for active enhancers. Enrichment analysis on the set of TCF4 targets identified numerous, highly significant functional clusters for pathways including nervous system development, ion transport and signal transduction and co-expression modules for genes associated with synaptic function and brain development. Importantly, we found that genes harboring de novo mutations in schizophrenia (P < 5.3 x 10-7), ASD (P < 2.5 x 10-4) and ID (P < 7.6 x 10-3) were also enriched among TCF4 targets. These data demonstrate that TCF4 binding sites are found in a large number of neuronal genes that include genetic risk factors for common neurodevelopmental disorders. Overall design: 2 TCF4 ChIP samples and 2 IgG negative controls