Kodali Sravan, Meyer-Nava Silvia, Landry Stephen, Chakraborty Arijita, Rivera-Mulia Juan Carlos, Feng Wenyi
Department of Biochemistry and Molecular Biology, Upstate Medical University, Syracuse, NY, United States.
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States.
Front Genet. 2022 Nov 24;13:907547. doi: 10.3389/fgene.2022.907547. eCollection 2022.
Common fragile sites (CFSs) are specific regions of all individuals' genome that are predisposed to DNA double strand breaks (DSBs) and undergo subsequent rearrangements. CFS formation can be induced by mild level of DNA replication stress, such as DNA polymerase inhibition or nucleotide pool disturbance. The mechanisms of CFS formation have been linked to DNA replication timing control, transcription activities, as well as chromatin organization. However, it is unclear what specific cis- or trans-factors regulate the interplay between replication and transcription that determine CFS formation. We recently reported genome-wide mapping of DNA DSBs under replication stress induced by aphidicolin in human lymphoblastoids for the first time. Here, we systematically compared these DSBs with regards to nearby epigenomic features mapped in the same cell line from published studies. We demonstrate that aphidicolin-induced DSBs are strongly correlated with histone 3 lysine 36 trimethylation, a marker for active transcription. We further demonstrate that this DSB signature is a composite effect by the dual treatment of aphidicolin and its solvent, dimethylsulfoxide, the latter of which potently induces transcription on its own. We also present complementing evidence for the association between DSBs and 3D chromosome architectural domains with high density gene cluster and active transcription. Additionally, we show that while DSBs were detected at all but one of the fourteen finely mapped CFSs, they were not enriched in the CFS core sequences and rather demarcated the CFS core region. Related to this point, DSB density was not higher in large genes of greater than 300 kb, contrary to reported enrichment of CFS sites at these large genes. Finally, replication timing analyses demonstrate that the CFS core region contain initiation events, suggesting that altered replication dynamics are responsible for CFS formation in relatively higher level of replication stress.
常见脆性位点（CFSs）是所有个体基因组中的特定区域，易发生DNA双链断裂（DSBs）并随后发生重排。CFS的形成可由轻度的DNA复制应激诱导，如DNA聚合酶抑制或核苷酸池紊乱。CFS形成的机制与DNA复制时间控制、转录活性以及染色质组织有关。然而，尚不清楚哪些特定的顺式或反式因子调节复制与转录之间的相互作用，从而决定CFS的形成。我们最近首次报道了在人淋巴母细胞中由阿非科林诱导的复制应激下DNA DSBs的全基因组图谱。在此，我们根据已发表研究中同一细胞系中绘制的附近表观基因组特征，系统地比较了这些DSBs。我们证明，阿非科林诱导的DSBs与组蛋白3赖氨酸36三甲基化密切相关，组蛋白3赖氨酸36三甲基化是活跃转录的标志物。我们进一步证明，这种DSB特征是阿非科林及其溶剂二甲基亚砜双重处理的复合效应，后者自身就能有效诱导转录。我们还提供了补充证据，证明DSBs与具有高密度基因簇和活跃转录的三维染色体结构域之间存在关联。此外，我们表明，虽然在14个精细定位的CFSs中，除了一个之外，在所有CFSs中都检测到了DSBs，但它们在CFS核心序列中并不富集，而是划定了CFS核心区域。与此相关的是，在大于300 kb的大基因中，DSB密度并不更高，这与报道的这些大基因中CFS位点的富集情况相反。最后，复制时间分析表明，CFS核心区域包含起始事件，这表明在相对较高水平的复制应激下，复制动力学的改变是CFS形成的原因。
