Programmed DNA double strand breaks fuel chromatin remodeling and potentiate stimulus-dependent gene induction

ABSTRACT: Neuronal activity critically depends on rapid transcriptional induction of early response genes (ERGs), yet how ERG promoters achieve fast, robust activation remains unclear. Here, we show that programmed DNA double-strand breaks (DSBs), catalyzed by topoisomerase 2β or introduced via CRISPR/Cas9, serve as a potent and surprisingly resilient mechanism to remodel three-dimensional (3D) genome architecture and drive ERG transcription. Using 4C-seq in both primary neurons and HEK293T cells, we find that a single DSB at an ERG promoter triggers an initial “exploratory” phase in which the promoter broadly expands its cis interactome—encompassing local enhancers as well as other chromatin states—to promote transcriptional activation. Contrary to the classical view of tightly pre-formed enhancer–promoter loops, these breaks enable flexible, compartment-confined sampling of the surrounding regulatory landscape. Strikingly, repeated rounds of DSB formation do not diminish but instead potentiate transcriptional output. Over time, the promoter’s cis interactions become more refined and “pruned,” coinciding with increased trans contacts, and these architectural changes persist long after the breaks have been repaired. Notably, even when DSB repair fidelity is low, ERG induction remains robust, underscoring a remarkable resilience in promoter function. Together, our findings reveal a novel model of transcriptional regulation in which transient DSBs act as powerful catalysts for dynamic and progressively fine-tuned 3D genome reorganization. This work broadens our understanding of how cells leverage controlled DNA breaks to support rapid transcriptional responses, while also facilitating adapted future responses.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE290726 | GEO | 2026/05/01

REPOSITORIES: GEO