Repair of Oxidative Genome Damage Associated with Gene Activation

修复与基因激活相关的氧化基因组损伤

• 批准号: 8639248
• 负责人: Sankar Mitra
• 金额: $ 30.31万
• 依托单位: METHODIST HOSPITAL RESEARCH INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-04-15 至 2018-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8639248
• 关键词: Alkaline Single-Cell Gel Electrophoresis Assay; Apoptosis; BCL2 gene; Binding; Biological Assay; Cancer Etiology; Cells; Chromatin; Chromatin Structure; Comet Assay; Complex; Cytosol; DNA Modification Process; Dioxygenases; Disease; Down-Regulation; Elements; Enhancers; Enzymes; Epigenetic Process; Estrogen Receptors; Estrogens; Excision; Family; Family member; Gene Activation; Gene Expression Regulation; Gene Targeting; Generations; Genes; Genetic Transcription; Genome; Health; Histone H3; Histones; Human Genome; Hydrogen Peroxide; In Vitro; Inflammation; Kinetics; Ligand Binding; Ligands; Link; Lysine; MCF7 cell; Malignant Neoplasms; Mediating; Methylation; Mitochondria; Monitor; N-terminal; Nuclear; Nucleic Acid Regulatory Sequences; Nucleotide Excision Repair; PARP inhibition; Pathway interactions; Process; Production; Proteins; Reaction; Reactive Oxygen Species; Reagent; Recruitment Activity; Relative (related person); Repair Complex; Repression; Resources; Respiration; Response Elements; Role; Signal Transduction; Single Strand Break Repair; Site; Specificity; System; Testing; Therapeutic; Toxic effect; Transcription Initiation; Transcriptional Activation; Tretinoin; Tumor Necrosis Factor-alpha; XRCC1 gene; arginyllysine; base; chromatin immunoprecipitation; demethylation; experience; gene repression; genome-wide; histone modification; human APEX1 protein; induced pluripotent stem cell; inhibitor/antagonist; mutant; new therapeutic target; oxidation; oxidative damage; prevent; promoter; protein complex; receptor; repaired; sensor

DESCRIPTION (provided by applicant): Reactive oxygen species (ROS), generated in mitochondria and cytosol, globally induce single-strand breaks (SSBs) and oxidized bases in the genome. Previously unrecognized, localized oxidative damage in promoter/enhancer regions, are induced by nuclear ROS produced during oxidative demethylation of methyl Lys/Arg in histones H3/H4 by lysine specific demethylase (LSD1in KMD family), and Jumanji (JMJ) family enzymes, and of methyl CpG sites in promoter sequences by TET dioxygenases during transcriptional activation. Ligands including estrogen (E2), retinoic acid (RA) and TNFα activate hundreds of target genes by binding to cognate receptors, which then form multi-protein complexes to unfold chromatin via complex histone modifications and CpG demethylation as a prerequisite for transcription initiation. We observed transient formation of single-strand breaks (SSBs), localized to the cis elements, presumably caused by ROS products of demethylases followed by repair which is initiated by SSB sensor PARP1, XRCC1 and end processing enzymes, e.g., APE1, PNKP. By monitoring site-specific repair using quantitative PCR, global genome repair by alkaline Comet assay and recruitment of repair proteins at the enhancer site via ChIP analysis, we observed that genome damage and repair rates are fast (completed in 10 min) for E2 activation of the BCL2 gene, moderate (~1 h) for TNFα activation of IL1α promoter and slow for RA activation of the RARβ2 gene (~4 h). Co-IP analysis showed that RA activation increased interaction between LSD1 and APE1and ChIP assay confirmed increased recruitment of PARP1 and other SSBR proteins at the enhancer site. This universal phenomenon of regulatory region specific damage induction and repair during gene activation has implications in damage signaling and toxicity which we will characterize by pursuing the following aims. Aim 1. To test the hypothesis that enhancer/promoter-specific oxidized bases and SSBs in BCL2, IL1β and RARβ2 genes and their repair are universally induced during gene activation. We will determine relative contribution of histone vs. CpG demethylation to the SSB production, elucidate the mechanism of recruitment of repair proteins and characterize the repair sub-pathways and end processing enzymes recruited at the SSB site. Aim 2. To test the hypothesis that repair proteins are recruited at promoter/enhancer sites by demethylases to form repair complexes. We will characterize complexes of demethylases with repair proteins, possibly including those of nucleotide excision repair. Aim 3. To unravel the role of PARP1 in repair of promoter/enhancer-specific SSBs induced during gene activation. We will test if PARP inhibition or depletion abrogates repair and transcriptional activation in all systems, and if SSB repair inhibition induces apoptosis after transcription activation only in replicating cells. Our state-of the-art approaches and sophisticated reagents will establish a new paradigm about gene activation-dependent genome damage and repair with therapeutic potential.

描述（由申请人提供）：活性氧（ROS）在线粒体和细胞质中产生，在基因组中全局诱导单链断裂（SSBs）和氧化碱基。在转录激活过程中，赖氨酸特异性去甲基酶（KMD家族中的lsd1）和Jumanji （JMJ）家族酶对组蛋白H3/H4中的甲基赖氨酸/精氨酸进行氧化去甲基化过程中产生的核ROS以及TET双加氧酶对启动子序列中的甲基CpG位点进行氧化去甲基化过程中产生的核ROS诱导了启动子/增强子区域的局部氧化损伤。包括雌激素（E2）、视黄酸（RA）和TNFα在内的配体通过与同源受体结合激活数百个靶基因，然后形成多蛋白复合物，通过复杂的组蛋白修饰和CpG去甲基化来展开染色质，这是转录起始的先决条件。我们观察到单链断裂（SSBs）的瞬时形成，定位于顺式元件，可能是由去甲基化酶的ROS产物引起的，随后由SSB传感器PARP1， XRCC1和末端加工酶（例如APE1， PNKP）启动修复。通过使用定量PCR监测位点特异性修复，使用碱性彗星测定全球基因组修复，以及通过ChIP分析在增强子位点募集修复蛋白，我们观察到E2激活BCL2基因的基因组损伤和修复速度快（在10分钟内完成），TNFα激活IL1α启动子的基因组损伤和修复速度中等（约1小时），RA激活RARβ2基因的基因组损伤和修复速度慢（约4小时）。Co-IP分析显示RA激活增加了LSD1和ape1之间的相互作用，ChIP实验证实PARP1和其他SSBR蛋白在增强子位点的募集增加。在基因激活过程中，这种调节区域特异性损伤诱导和修复的普遍现象对损伤信号传导和毒性有影响，我们将通过追求以下目标来描述。目的1。为了验证BCL2、il - 1β和rar - β2基因中增强子/启动子特异性氧化碱基和SSBs及其修复在基因激活过程中被普遍诱导的假设。我们将确定组蛋白和CpG去甲基化对SSB产生的相对贡献，阐明修复蛋白的募集机制，表征修复亚途径和SSB位点募集的末端加工酶。目标2。为了验证修复蛋白通过去甲基化酶在启动子/增强子位点募集形成修复复合物的假设。我们将描述去甲基化酶与修复蛋白的复合物，可能包括核苷酸切除修复的复合物。目标3。揭示PARP1在基因激活过程中诱导的启动子/增强子特异性SSBs修复中的作用。我们将测试PARP抑制或耗尽是否在所有系统中消除修复和转录激活，以及SSB修复抑制是否仅在复制细胞中诱导转录激活后的凋亡。我们的状态