Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis
Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis
复制标题
DOI：
10.1073/pnas.1603388113
复制
发表时间：
2016-04-12
影响因子：
11.1
通讯作者：
Sancar, Aziz
中科院分区：
文献类型：
--
作者：
Adar, Sheera;Hu, Jinchuan;Sancar, Aziz
我们最近开发了一种用于绘制DNA切除修复的高分辨率全基因组检测方法，称为eXcision Repair-sequencing（XR-seq），现在已经使用XR-seq来确定基因组的哪些区域在紫外线暴露后很快就会修复，哪些区域稍后修复。随着时间的推移，我们测量了正常人皮肤成纤维细胞中环丁烷嘧啶二聚体（CPD）（1，4，8，16，24和48 h）和（6-4）嘧啶嘧啶酮光产物[（6-4）PP]（5和20 min以及1，2和4 h）的UV诱导损伤修复。每种类型的损伤都有不同的修复动力学。（6-4）PPs在UV处理后5 min就被检测到，大部分修复在4 h完成。我们先前发现的CPD与转录密切相关，其修复速度较慢，并且在某些区域甚至在UV照射后持续2天。我们将我们的结果与DNA元素百科全书中关于组蛋白修饰、染色质状态和转录的数据进行了比较。对于这两种损伤类型，以及转录偶联和一般切除修复，最早的修复优先发生在活跃和开放的染色质状态。相反，在被分类为“异染色质”和“抑制”的区域中的修复在早期时间点相对较低，修复持续到晚期时间点。DNA复制过程中残留的损伤增加了诱变的风险。事实上，晚期修复区域与更高水平的癌症相关突变相关。总之，我们表明XR-seq是研究染色质状态，DNA修复，基因组稳定性，诱变和致癌之间关系的有力方法。
We recently developed a high-resolution genome-wide assay for mapping DNA excision repair named eXcision Repair-sequencing (XR-seq) and have now used XR-seq to determine which regions of the genome are subject to repair very soon after UV exposure and which regions are repaired later. Over a time course, we measured repair of the UV-induced damage of cyclobutane pyrimidine dimers (CPDs) (at 1, 4, 8, 16, 24, and 48 h) and (6-4) pyrimidinepyrimidone photoproducts [(6-4) PPs] (at 5 and 20 min and 1, 2, and 4 h) in normal human skin fibroblasts. Each type of damage has distinct repair kinetics. The (6-4) PPs are detected as early as 5 min after UV treatment, with the bulk of repair completed by 4 h. Repair of CPDs, which we previously showed is intimately coupled to transcription, is slower and in certain regions persists even 2 d after UV irradiation. We compared our results to the Encyclopedia of DNA Elements data regarding histone modifications, chromatin state, and transcription. For both damage types, and for both transcription-coupled and general excision repair, the earliest repair occurred preferentially in active and open chromatin states. Conversely, repair in regions classified as "heterochromatic" and "repressed" was relatively low at early time points, with repair persisting into the late time points. Damage that remains during DNA replication increases the risk for mutagenesis. Indeed, late-repaired regions are associated with a higher level of cancer-linked mutations. In summary, we show that XR-seq is a powerful approach for studying relationships among chromatin state, DNA repair, genome stability, mutagenesis, and carcinogenesis.