Persistent chromatin alterations and gene expression reprogramming follow widespread DNA damage in glioblastoma

Abstract

DNA damage from routine cellular processes or exogenous insults can have a lasting impact on gene regulation beyond genetic mutations1, 2, 3, 4–5. The prevailing paradigm for the consequences of DNA damage repair revolves around restoration of the original genetic sequence, but long-term changes in chromatin configuration, gene expression and DNA modifications have not been analyzed. We introduce numerous, simultaneous Cas9-mediated DNA double strand breaks (DSBs) at defined locations in human glioblastoma cells and track both non-genetic and genetic alterations over time. Megabase-scale genomic alterations that endured two weeks after the initial damage were detected, involving a shift from transiently increased intra-TAD interactions to persistent long range cis and trans contacts, alterations in gene-expression and associated large structural variations. These findings reveal that widespread DNA damage, such as chemotherapy or radiotherapy, can trigger long-term genetic and non-genetic modifications which alter cellular function and may impact tumor outcome and the emergence of resistant cells. How DNA damage reshapes cancer cells beyond genetic mutations is poorly understood. Here, the authors show that DNA double-strand breaks in glioblastoma cells trigger lasting non-genetic changes in 3D genome folding, gene expression and DNA modifications that persist for weeks.