Abstract
AbstractEndogenous DNA double-strand breaks (DSBs) occurring in neural cells have been implicated in the pathogenesis of neurodevelopmental disorders (NDDs). Currently, a genomic map of endogenous DSBs arising during human neurogenesis is missing. Here, we applied in-suspension Breaks Labeling In Situ and Sequencing (sBLISS), RNA-Seq, and Hi-C to chart the genomic landscape of DSBs and relate it to gene expression and genome architecture in 2D cultures of human neuroepithelial stem cells (NES), neural progenitor cells (NPC), and post-mitotic neural cells (NEU). Endogenous DSBs were enriched at the promoter and along the gene body of transcriptionally active genes, at the borders of topologically associating domains (TADs), and around chromatin loop anchors. NDD risk genes harbored significantly more DSBs in comparison to other protein-coding genes, especially in NEU cells. We provide sBLISS, RNA-Seq, and Hi-C datasets for each differentiation stage, and all the scripts needed to reproduce our analyses. Our datasets and tools represent a unique resource that can be harnessed to investigate the role of genome fragility in the pathogenesis of NDDs.
Funder
Karolinska Institutet Strategic Research Area Neuroscience (StratNeuro) Postdoctoral Fellowship 2019
Svenska Sällskapet för Medicinsk Forskning
EC | Horizon 2020 Framework Programme
Vetenskapsrådet
--Karolinska Institutet KID Grants 2017 --Ragnar Soderberg Foundation
Publisher
Springer Science and Business Media LLC
Subject
Library and Information Sciences,Statistics, Probability and Uncertainty,Computer Science Applications,Education,Information Systems,Statistics and Probability
Cited by
3 articles.
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