LAUSR

Background The application of human induced Pluripotent Stem Cells (iPSCs)-differentiated neurons has served as a promising model for gaining insights into the molecular and cellular mechanisms of genetic risk for mental disorders. Multiple factors determine the fate and trajectory of neuronal cell differentiation, of which transcriptional regulation plays a major role. Chromatin accessibility (openness) to Transcription Factors (TF) strongly influences gene transcription and cell differentiation. However, the dynamic changes of open chromatin and the TF networks during neuronal differentiation from iPSCs are poorly understood. Methods Here, we performed a global mapping of Open Chromatin Regions (OCRs) using the Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) at different cell stages of glutamatergic neuronal differentiation, examined the correlation of changes of open chromatin and mRNA abundances (assayed by RNA-Seq), and constructed the neuronal stage-specific TF networks through a genome-wide inference of TF-binding footprints in OCRs. Results We found that OCRs were highly dynamic during neuronal differentiation, and more importantly that OCR accessibility at core promoter regions was positively correlated with mRNA abundances at their respective cell stages. Furthermore, we found that the dynamic changes of OCRs during neuronal differentiation were accompanied by the binding events of cell stage-specific TFs. As expected, binding footprints of OCT4 and NANOG, genes that encode pluripotent stem cell-specific markers, are most enriched in iPSCs. Intriguingly, binding footprints of NEUROD1 and NEUROG2, the two TFs that have been reported to rapidly induce high efficient conversion of iPSCs to excitatory neurons, are among those most enriched in the relatively mature neurons. Discussion Further TF network analysis based on the inferred TF binding footprints in OCRs successfully identified core TF networks and their master regulators for different neuronal stages. Interestingly, both NEUROD1 and NEUROG2 are in the same core TF network specific to more mature neurons, suggesting their pivotal role in epigenetic control of neuronal differentiation and maturation.