School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
Mol Biol Rep. 2019 Aug;46(4):3731-3745. doi: 10.1007/s11033-019-04815-6. Epub 2019 Apr 29.
For ionising radiation (IR)-induced cellular toxicity, DNA cleavage is thought to be a crucial step. In this paper, the genome-wide DNA sequence preference of gamma radiation-induced cleavage was investigated in purified human DNA. We utilised Illumina short read technology and over 80 million double-strand breaks (DSBs) were analysed in this study. The frequency of occurrence of individual nucleotides at the 50,000 most frequently cleaved sites was calculated and C nucleotides were found to be most prevalent at the cleavage site, followed by G and T, with A being the least prevalent. 5'-CC and 5'-CC dinucleotides (where * is the cleavage site) were found to be the present at the highest frequency at the cleavage site; while it was 5'-CCC for trinucleotides and 5'-GCCC and 5'-CCCC for tetranucleotides. The frequency of occurrence of individual nucleotides at the most frequently cleaved sites was determined and the nucleotides in the sequence 5'-GGCMH (where M is A or C, H is any nucleotide except G) were found to occur most frequently for DNA that was treated with endonuclease IV (to remove blocking 3'-phosphoglycolate termini); and 5'-GSC*MH (where S is G or C) for non-endonuclease IV-treated DNA. It was concluded that GC-rich sequences were preferentially targeted for cleavage by gamma irradiation. This was the first occasion that an extensive examination of the genome-wide DNA sequence preference of IR-induced DSBs has been performed.
对于电离辐射（IR）诱导的细胞毒性，DNA 断裂被认为是一个关键步骤。在本文中，我们研究了γ射线诱导的断裂在纯化的人 DNA 中的全基因组 DNA 序列偏好。我们利用 Illumina 短读技术，在这项研究中分析了超过 8000 万个双链断裂（DSB）。在 50000 个最常断裂的位点中，计算了每个核苷酸的出现频率，结果发现 C 核苷酸在断裂位点最为常见，其次是 G 和 T，而 A 则最少见。在断裂位点，发现 5'-CC 和 5'-CC二核苷酸（其中是断裂位点）出现频率最高；而三核苷酸为 5'-CCC，四核苷酸为 5'-GCCC 和 5'-CCCC。在最常断裂的位点确定了每个核苷酸的出现频率，发现在用内切酶 IV（去除 3'-磷酸甘油酸末端的阻断）处理的 DNA 中，序列 5'-GGCMH（其中 M 是 A 或 C，H 是除 G 以外的任何核苷酸）的核苷酸出现频率最高；而对于未经内切酶 IV 处理的 DNA，序列 5'-GSCMH（其中 S 是 G 或 C）的核苷酸出现频率最高。结论是富含 GC 的序列优先被γ辐射靶向断裂。这是首次对 IR 诱导的 DSB 全基因组 DNA 序列偏好进行广泛检查。
