Profiling of endogenous DNA double-strand breaks during neural cell fate determination using sBLISS.

Abstract: Naturally occurring endogenous DNA double-strand breaks (DSBs) have been detected in neuronal cells and implicated in the pathogenesis of neurodevelopmental disorders (NDDs). Here, we describe a genome-wide atlas of endogenous DSBs mapped by suspension Breaks Labeling In Situ and Sequencing (sBLISS) in proliferating neuroepithelial stem (NES) cells in culture, neural progenitor cells (NPC) after 6 days of NES differentiation towards neurons, and post-mitotic neurons (NEU) after 35 days of differentiation. Genome-wide DSB maps were highly reproducible between biological replicates of the same cell type, at multiple resolutions down to 10 kilobases (kb). To validate our datasets, we examined the distribution of DSBs in different genomic regions, demonstrating that endogenous DSBs are enriched around transcriptionally active promoters and chromatin loop anchors mapped by high-throughput chromosome conformation capture (Hi-C), in line with previous findings in different cell types. Lastly, we assessed DSBs in the promoter region and along the gene body of NDD risk genes, demonstrating that these genes have a significantly higher burden of DSBs compared to all other genes in all the three cell types examined, confirming prior observations using different DSB-detection strategies. Our datasets represent a valuable resource for exploring genome fragility during neural cell fate determination and assessing its contribution to the pathogenesis of neurodevelopmental disorders. <br> Data: This repository contains processed data files from sBLISS performed on three different stages of neuronal differentiation (2 replicates each). Raw data is available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA798046