Neurons, terminally differentiated post-mitotic cells, face a remarkable challenge: throughout life, they must maintain a gene expression program that defines cellular identity while simultaneously allowing for transcriptional plasticity in response to a changing environment. There is robust literature demonstrating that neurons initiate a transcriptional response to neuronal activity within minutes, leading to the expression of immediate early genes (IEGs), including Fos, Arc, Jun, and Npas4. Subsequently, IEGs lead to the expression of more cell-type specific late response genes, such as Bdnf, Igf1, Homer1, Dnmt3a, Hdac5, and Kdm1a, which are diverse and less well characterized [1]. Neurons also stably retain information through epigenetic mechanisms, including histone modifications and molecular changes to DNA itself, either through DNA methylation and hydroxymethylation or other more recently discovered epigenetic modifications [2].
In the past 10 years, several groups have published convincing data that neurons, in response to activity, produce transient double-strand breaks (DSBs) in DNA, which is considered to be a harmful process associated with aging and aging-related disorders. This idea was initially based upon the observation of an accumulation of phosphorylation of histone variant H2A.X (termed γ-H2A.X), a highly specific marker for DSBs, in rat cortical cultures in vitro [3]. The accumulation of γ-H2A.X was subsequently shown to occur in vivo, in several different neuron types, in response to both physiological and optogenetic stimulation [4]. More directly, Madabhushi et al. showed that neuronal activity-induced DSB formation mostly in the promoters of IEGs and artificially targeted DSBs in IEGs in vitro were sufficient to increase IEG expression, in the absence of neuronal activity (Fig. 1).
Fig. 1. Neurons produce double-stranded DNA breaks (DSBs) in response to activity.
Several studies have demonstrated that the formation of activity-induced DSBs occurs in the promoters of immediate early genes, such as Fos, Arc, Jun, and Npas4, where TopoIIβ relieves torsional stress of DNA induced by RNA polymerase during transcription. This leads to transcription of these genes and drives expression of downstream genes, including Bdnf, Igf1, and Homer1, and potentially alters neuronal plasticity.
The formation of DSBs and subsequent DNA repair may offer neurons a kinetic advantage to permit rapid transcriptional responses. It is hypothesized that the release of energy from relaxing supercoiled DNA may allow for the rapid initiation of a poised transcriptional complex of IEGs. Predicted binding sites for the protein CTCF, an architectural protein that produces chromatin loops, are highly enriched for the binding locations of TopoIIβ, a DNA topoisomerase involved in the relief of torsional stress during transcription, in cultured neurons. This suggests a model in which topological constraints cause RNA polymerase to pause at IEG enhancers and promoters where activity-induced transient cleavage of DNA allows for rapid IEG transcription [5].
Maintenance of DNA integrity is critical in all cells, as mutations can lead to loss of information, triggering of cell death pathways, or uncontrolled growth. DSBs are particularly perilous, as they can lead to insertions, duplications, or translocations [6]. The physiological role of DSB formation in neurons may explain the association between mutations in DNA repair pathways and neurodegeneration. It is tantalizing to suppose that the need for physiological DSB induction makes neurons uniquely susceptible to deficits in DNA repair processes. Future studies of the brain-wide dynamics of highly programmed DNA DSB formation using tools like CRISPR will offer an exciting entry point to determine its scope and function in neuronal activity-induced gene expression that contribute to higher order brain functions including neural plasticity and long-term information storage.
Author contributions
RJF conceived of the topic for this article; RJF and JS co-wrote the article; and JS produced the figure.
Funding
RJF is funded through the HMS Broderick Phytocannabinoid Research grant. JS is funded through R01MH108665 and R01MH123993.
Competing interests
The authors declare no competing interests.
Footnotes
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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