Department of Biology, University of Naples 'Federico II', Naples, Italy.
Department of Molecular Medicine and Medical Biotechnologies, University of Naples 'Federico II', Naples, Italy.
Nucleic Acids Res. 2022 Apr 8;50(6):3292-3306. doi: 10.1093/nar/gkac143.
8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), a major product of the DNA oxidization process, has been proposed to have an epigenetic function in gene regulation and has been associated with genome instability. NGS-based methodologies are contributing to the characterization of the 8-oxodG function in the genome. However, the 8-oxodG epigenetic role at a genomic level and the mechanisms controlling the genomic 8-oxodG accumulation/maintenance have not yet been fully characterized. In this study, we report the identification and characterization of a set of enhancer regions accumulating 8-oxodG in human epithelial cells. We found that these oxidized enhancers are mainly super-enhancers and are associated with bidirectional-transcribed enhancer RNAs and DNA Damage Response activation. Moreover, using ChIA-PET and HiC data, we identified specific CTCF-mediated chromatin loops in which the oxidized enhancer and promoter regions physically associate. Oxidized enhancers and their associated chromatin loops accumulate endogenous double-strand breaks which are in turn repaired by NHEJ pathway through a transcription-dependent mechanism. Our work suggests that 8-oxodG accumulation in enhancers-promoters pairs occurs in a transcription-dependent manner and provides novel mechanistic insights on the intrinsic fragility of chromatin loops containing oxidized enhancers-promoters interactions.
8-氧代-7,8-二氢-2'-脱氧鸟苷（8-oxodG）是 DNA 氧化过程的主要产物，据推测它在基因调控中具有表观遗传功能，并与基因组不稳定性有关。基于 NGS 的方法学正在帮助我们描述 8-oxodG 在基因组中的功能。然而，8-oxodG 在基因组水平上的表观遗传作用以及控制基因组 8-oxodG 积累/维持的机制尚未得到充分描述。在本研究中，我们报告了一组在人类上皮细胞中积累 8-oxodG 的增强子区域的鉴定和特征。我们发现这些氧化增强子主要是超级增强子，并与双向转录的增强子 RNA 和 DNA 损伤反应激活有关。此外，我们使用 ChIA-PET 和 HiC 数据，鉴定了特定的 CTCF 介导的染色质环，其中氧化的增强子和启动子区域物理关联。氧化的增强子及其相关的染色质环积累内源性双链断裂，这些断裂通过转录依赖性机制通过非同源末端连接（NHEJ）途径进行修复。我们的工作表明，增强子-启动子对中 8-oxodG 的积累是转录依赖性的，并为含有氧化增强子-启动子相互作用的染色质环的固有脆弱性提供了新的机制见解。
