Single-cell chromatin accessibility identifies enhancer networks driving gene expression during spinal cord development in mouse.

Spinal cord development is precisely orchestrated by spatiotemporal gene regulatory programs. However, the underlying epigenetic mechanisms remain largely elusive. Here, we profiled single-cell chromatin accessibility landscapes in mouse neural tubes spanning embryonic days 9.5–13.5. We identified neuronal-cell-cluster-specific cis -regulatory elements in neural progenitors and neurons. Furthermore, we applied a novel computational method, eNet, to build enhancer networks by integrating single-cell chromatin accessibility and gene expression data and identify the hub enhancers within enhancer networks. It was experimentally validated in vivo for Atoh1 that knockout of the hub enhancers, but not the non-hub enhancers, markedly decreased Atoh1 expression and reduced dp1/dI1 cells. Together, our work provides insights into the epigenetic regulation of spinal cord development and a proof-of-concept demonstration of enhancer networks as a general mechanism in transcriptional regulation. [Display omitted] • Single-cell chromatin accessibility profiling charts mouse spinal cord development • Enhancer networks control master regulators during neuronal development • Network hub enhancers are potentially key cis- elements to control gene expression • In vivo Atoh1 enhancer knockout demonstrates functional hierarchy of enhancer network Shu and Hong et al. provide single-cell chromatin accessibility analyses of developing mouse spinal cord and identify cis -regulatory elements and regulators for neural cells. Using these data, they define enhancer networks controlling master regulators during spinal cord development and experimentally validate Atoh1 enhancers through in vivo perturbation as a proof of concept. [ABSTRACT FROM AUTHOR]