Analysis of SOD1 binding sites by next generation sequencing under different redox environments

We report the application of ChIP-Seq technology for analyzing the DNA binding sites of SOD1 in the nucleus of HeLa cells. By obtaining a plenty of sequence from chromatin immunoprecipitated DNA, we generated genome-wide DNA binding sites of SOD1. After sequencing of ChIP samples, 42,737,195, 49,950,032, and 38,825,768 clean reads for control group, H2O2 treated group and LD100 (a specific inhibitor of SOD1) treated group were obtained through trimming the raw reads. We find that SOD1 occupies DNA sites with distinct sequence preference in the nucleus. The treatment with either H2O2 or LD100 was found to decrease the strength of SOD1 binding to DNA, indicating that the H2O2 exposure- or SOD1 inhibition-mediated redox dyshomeostasis may result in decreased genes that are reasonably regulated through alteration of SOD1 structures compared to control. Overall design: Examination of SOD1 binding to DNA in the nucleus under different redox conditions

本研究报道了利用染色质免疫共沉淀测序（ChIP-Seq）技术分析海拉细胞（HeLa cells）细胞核内超氧化物歧化酶1（SOD1）DNA结合位点的相关工作。通过从染色质免疫沉淀获取的DNA中获得足量序列，我们构建了SOD1全基因组范围的DNA结合位点数据集。对ChIP样本完成测序后，通过对原始读段（raw reads）进行修剪质控，我们分别获得了对照组、过氧化氢（H₂O₂）处理组以及SOD1特异性抑制剂LD100处理组的清洁读段（clean reads），数量依次为42,737,195、49,950,032和38,825,768。研究发现，SOD1在细胞核内结合的DNA位点具有显著的序列偏好性。实验结果显示，经H₂O₂或LD100处理后，SOD1与DNA的结合强度均出现下降；这表明，相较于对照组，H₂O₂暴露或SOD1抑制所介导的氧化还原稳态失衡，可能通过改变SOD1的结构，导致其正常调控的基因表达水平下调。实验整体设计：考察不同氧化还原条件下细胞核内SOD1与DNA的结合情况。