Paint a self-portrait, build a house? If, instead, your more achievable New Year’s resolution was to be more active, new and exciting findings on how the abundance of single-strand DNA breaks (SSBs) at neuronal enhancers represents an intermediate of active DNA demethylation will be right down your alley!
Researchers led by Wei Wu and André Nussenzweig (National Cancer Institute NIH) (and others) had previously reported significant levels of SSBs and DNA repair activity at neuronal gene enhancers in post-mitotic neurons using SAR-seq (DNA synthesis associated with repair sequencing). In their follow-up, DNA demethylation-focused study, the authors aimed to understand the source of SSBs and their physiological relevance to explore why cells concentrate repair machinery to these hotspots in post-mitotic cells.
Let’s hear from Wang, Wu, Callen, and colleagues on how DNA SSBs to ensure cell function:
- Active DNA demethylation mediated by ten-eleven translocation (TET) methylcytosine dioxygenases generates SSBs at lineage-specifying enhancers in post-mitotic neurons as an intermediate of oxidized methylcytosines (5fC and 5caC) removal by thymine DNA glycosylase (TDG), which then induces “long patch” base excision repair (BER)
- TDG-deficient neurons accumulate 5fC/5caC but display lower SSB levels at enhancers, suggesting that SSB formation requires TDG
- Although pre-B cells lack neuron-like DNA repair foci, TET2 activity at myeloid enhancers during pre-B cell-to-macrophage transdifferentiation promotes TDG-dependentactive DNA demethylation and SSB accumulation and then induces short-patch BER
- Importantly, TDG-deficient macrophages display 5fC/5caC accumulation and reduced phagocytosis, suggesting that cell function requires DNA demethylation and SSB formation
- Furthermore, TDG-deficient pre-B cells fail to upregulate macrophage differentiation-associated genes lying close to lineage-specifying enhancers undergoing DNA repair during transdifferentiation
- Exposure to cytosine analogs increases DNA synthesis-associated long-patch BER at lineage-specifying enhancers in neurons and macrophages after incorporation into DNA during short-patch BER
- Treatment of neurons with the cytosine analog Ara-C (a chemotherapeutic that causes neurotoxicity) prompts an initial p53 transcriptional response and then induces neuronal death after sustained exposure
- TDG-loss prevents Ara-C–induced cell death, suggesting that TET-initiated active DNA demethylation correlates with the onset of cytosine analog-induced neurotoxicity (commonly called “chemobrain“)
These findings show that SSBs represent a critical intermediate state of the DNA demethylation process that helps to ensure cell function and identity. It also highlights that the above process could be linked to chemobrain, where the development of therapeutics targeting this pathway could benefit patients.
Get active with DNA demethylation in Science, December 2022.