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An Enzyme-Linked Immunosorbent Assay for the Detection of Mitochondrial DNA-Protein Cross-Links from Mammalian Cells. 用于检测哺乳动物细胞线粒体dna -蛋白交联的酶联免疫吸附试验。
DNA
Pub Date : 2022-12-01 DOI: 10.3390/dna2040019
Wenyan Xu, Linlin Zhao

DNA-Protein cross-links (DPCs) are cytotoxic DNA lesions with a protein covalently bound to the DNA. Although much has been learned about the formation, repair, and biological consequences of DPCs in the nucleus, little is known regarding mitochondrial DPCs. This is due in part to the lack of robust and specific methods to measure mitochondrial DPCs. Herein, we reported an enzyme-linked immunosorbent assay (ELISA)-based method for detecting mitochondrial DPCs formed between DNA and mitochondrial transcription factor A (TFAM) in cultured human cells. To optimize the purification and detection workflow, we prepared model TFAM-DPCs via Schiff base chemistry using recombinant human TFAM and a DNA substrate containing an abasic (AP) lesion. We optimized the isolation of TFAM-DPCs using commercial silica gel-based columns to achieve a high recovery yield for DPCs. We evaluated the microplate, DNA-coating solution, and HRP substrate for specific and sensitive detection of TFAM-DPCs. Additionally, we optimized the mtDNA isolation procedure to eliminate almost all nuclear DNA contaminants. For proof of concept, we detected the different levels of TFAM-DPCs in mtDNA from HEK293 cells under different biological conditions. The method is based on commercially available materials and can be amended to detect other types of DPCs in mitochondria.

DNA-蛋白质交联(DPCs)是一种细胞毒性的DNA损伤,蛋白质与DNA共价结合。尽管人们对细胞核中DPCs的形成、修复和生物学后果了解甚多,但对线粒体DPCs知之甚少。这部分是由于缺乏可靠和特定的方法来测量线粒体DPCs。在此,我们报道了一种基于酶联免疫吸附试验(ELISA)的方法,用于检测培养的人细胞中DNA和线粒体转录因子A (TFAM)之间形成的线粒体DPCs。为了优化纯化和检测流程,我们利用重组人TFAM和含有碱性(AP)病变的DNA底物,通过希夫碱化学制备了模型TFAM- dpcs。我们优化了用硅胶基柱分离TFAM-DPCs的方法,以获得高回收率的DPCs。我们评估了微孔板、dna包被液和HRP底物对TFAM-DPCs的特异性和敏感性。此外,我们优化了mtDNA的分离程序,以消除几乎所有的核DNA污染物。为了证明这一概念,我们检测了不同生物学条件下HEK293细胞mtDNA中不同水平的TFAM-DPCs。该方法基于商业上可用的材料,并且可以修改以检测线粒体中其他类型的DPCs。
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引用次数: 4
Size- and Stereochemistry-Dependent Transcriptional Bypass of DNA Alkyl Phosphotriester Adducts in Mammalian Cells. 哺乳动物细胞中DNA烷基磷酸三酯加合物的大小和立体化学依赖性转录旁路。
DNA
Pub Date : 2022-12-01 DOI: 10.3390/dna2040016
Ying Tan, Jiabin Wu, Garrit Clabaugh, Lin Li, Hua Du, Yinsheng Wang

Environmental, endogenous and therapeutic alkylating agents can react with internucleotide phosphate groups in DNA to yield alkyl phosphotriester (PTE) adducts. Alkyl-PTEs are induced at relatively high frequencies and are persistent in mammalian tissues; however, their biological consequences in mammalian cells have not been examined. Herein, we assessed how alkyl-PTEs with different alkyl group sizes and stereochemical configurations (S P and R P diastereomers of Me and nPr) affect the efficiency and fidelity of transcription in mammalian cells. We found that, while the R P diastereomer of Me- and nPr-PTEs constituted moderate and strong blockages to transcription, respectively, the S P diastereomer of the two lesions did not appreciably perturb transcription efficiency. In addition, none of the four alkyl-PTEs induced mutant transcripts. Furthermore, polymerase η assumed an important role in promoting transcription across the S P-Me-PTE, but not any of other three lesions. Loss of other translesion synthesis (TLS) polymerases tested, including Pol κ, Pol ι, Pol ξ and REV1, did not alter the transcription bypass efficiency or mutation frequency for any of the alkyl-PTE lesions. Together, our study provided important new knowledge about the impact of alkyl-PTE lesions on transcription and expanded the substrate pool of Pol η in transcriptional bypass.

环境、内源性和治疗性烷基化剂可以与DNA中的核苷酸间磷酸基团反应生成烷基磷酸三酯(PTE)加合物。烷基pte的诱导频率相对较高,并在哺乳动物组织中持续存在;然而,它们在哺乳动物细胞中的生物学后果尚未得到检验。在此,我们评估了具有不同烷基大小和立体化学构型(Me和nPr的S P和R P非对映体)的烷基- pte如何影响哺乳动物细胞中的转录效率和保真度。我们发现,虽然Me-和npr - pte的rp非对映体分别构成中度和强烈的转录阻断,但两种病变的S P非对映体并未明显干扰转录效率。此外,四种烷基pte均未诱导突变体转录本。此外,聚合酶η在促进S - P-Me-PTE的转录中发挥了重要作用,但在其他三种病变中没有作用。其他翻译合成(TLS)聚合酶的缺失,包括Pol κ、Pol ι、Pol ξ和REV1,没有改变任何烷基pte病变的转录旁路效率或突变频率。总之,我们的研究为烷基- pte损伤对转录的影响提供了重要的新知识,并扩大了转录旁路中Pol η的底物池。
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引用次数: 3
Mitochondrial DNA: Consensuses and Controversies. 线粒体DNA:共识和争议。
DNA
Pub Date : 2022-06-01 Epub Date: 2022-06-10 DOI: 10.3390/dna2020010
Inna Shokolenko, Mikhail Alexeyev

In the course of its short history, mitochondrial DNA (mtDNA) has made a long journey from obscurity to the forefront of research on major biological processes. mtDNA alterations have been found in all major disease groups, and their significance remains the subject of intense research. Despite remarkable progress, our understanding of the major aspects of mtDNA biology, such as its replication, damage, repair, transcription, maintenance, etc., is frustratingly limited. The path to better understanding mtDNA and its role in cells, however, remains torturous and not without errors, which sometimes leave a long trail of controversy behind them. This review aims to provide a brief summary of our current knowledge of mtDNA and highlight some of the controversies that require attention from the mitochondrial research community.

在其短暂的历史过程中,线粒体DNA (mtDNA)经历了漫长的旅程,从默默无闻到主要生物过程的研究前沿。在所有主要疾病组中都发现了mtDNA的改变,其意义仍然是深入研究的主题。尽管取得了显著的进展,但我们对mtDNA生物学的主要方面,如其复制、损伤、修复、转录、维持等的理解仍令人沮丧地有限。然而,更好地理解mtDNA及其在细胞中的作用的道路仍然是痛苦的,并非没有错误,有时会留下一长串争议。这篇综述的目的是提供我们目前对线粒体dna的知识的简要总结,并强调一些需要引起线粒体研究界注意的争议。
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引用次数: 8
Nucleases and Co-Factors in DNA Replication Stress Responses. DNA复制应激反应中的核酸酶和共因子。
DNA
Pub Date : 2022-03-01 DOI: 10.3390/dna2010006
Jac A Nickoloff, Neelam Sharma, Lynn Taylor, Sage J Allen, Robert Hromas

DNA replication stress is a constant threat that cells must manage to proliferate and maintain genome integrity. DNA replication stress responses, a subset of the broader DNA damage response (DDR), operate when the DNA replication machinery (replisome) is blocked or replication forks collapse during S phase. There are many sources of replication stress, such as DNA lesions caused by endogenous and exogenous agents including commonly used cancer therapeutics, and difficult-to-replicate DNA sequences comprising fragile sites, G-quadraplex DNA, hairpins at trinucleotide repeats, and telomeres. Replication stress is also a consequence of conflicts between opposing transcription and replication, and oncogenic stress which dysregulates replication origin firing and fork progression. Cells initially respond to replication stress by protecting blocked replisomes, but if the offending problem (e.g., DNA damage) is not bypassed or resolved in a timely manner, forks may be cleaved by nucleases, inducing a DNA double-strand break (DSB) and providing a means to accurately restart stalled forks via homologous recombination. However, DSBs pose their own risks to genome stability if left unrepaired or misrepaired. Here we focus on replication stress response systems, comprising DDR signaling, fork protection, and fork processing by nucleases that promote fork repair and restart. Replication stress nucleases include MUS81, EEPD1, Metnase, CtIP, MRE11, EXO1, DNA2-BLM, SLX1-SLX4, XPF-ERCC1-SLX4, Artemis, XPG, and FEN1. Replication stress factors are important in cancer etiology as suppressors of genome instability associated with oncogenic mutations, and as potential cancer therapy targets to enhance the efficacy of chemo- and radiotherapeutics.

DNA复制压力是一个持续的威胁,细胞必须设法增殖并保持基因组完整性。DNA复制应激反应是更广泛的DNA损伤反应(DDR)的一个子集,当DNA复制机制(复制子体)在S期被阻断或复制叉塌陷时,它就会发挥作用。复制应激有许多来源,如内源性和外源性因素引起的DNA损伤,包括常用的癌症治疗剂,以及难以复制的DNA序列,包括脆弱位点、G-quadraplex DNA、三核苷酸重复的发夹和端粒。复制应激也是反向转录和复制之间冲突的结果,以及失调复制起源发射和分叉进展的致癌应激。细胞最初通过保护被阻断的复制体来应对复制应激,但如果没有及时绕过或解决问题(例如DNA损伤),叉可能会被核酸酶切割,从而诱导DNA双链断裂(DSB),并通过同源重组提供准确重启停滞叉的手段。然而,如果未修复或修复不当,DSBs也会对基因组稳定性造成风险。在这里,我们重点关注复制应激反应系统,包括DDR信号、分叉保护和通过核酸酶进行的分叉处理,以促进分叉修复和重启。复制应激核酸酶包括MUS81、EEPD1、Metnase、CtIP、MRE11、EXO1、DNA2-BLM、SLX1-SLX4、XPF-ERCC1-SLX4,Artemis、XPG和FEN1。复制应激因子作为与致癌突变相关的基因组不稳定性的抑制剂,以及作为提高化疗和放射治疗效果的潜在癌症治疗靶点,在癌症病因中是重要的。
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引用次数: 0
Small RNAs Worm Up Transgenerational Epigenetics Research. 小核糖核酸催生跨代表观遗传学研究
DNA
Pub Date : 2021-12-01 Epub Date: 2021-09-29 DOI: 10.3390/dna1020005
Alla Grishok

DNA is central to the propagation and evolution of most living organisms due to the essential process of its self-replication. Yet it also encodes factors that permit epigenetic (not included in DNA sequence) flow of information from parents to their offspring and beyond. The known mechanisms of epigenetic inheritance include chemical modifications of DNA and chromatin, as well as regulatory RNAs. All these factors can modulate gene expression programs in the ensuing generations. The nematode Caenorhabditis elegans is recognized as a pioneer organism in transgenerational epigenetic inheritance research. Recent advances in C. elegans epigenetics include the discoveries of control mechanisms that limit the duration of RNA-based epigenetic inheritance, periodic DNA motifs that counteract epigenetic silencing establishment, new mechanistic insights into epigenetic inheritance carried by sperm, and the tantalizing examples of inheritance of sensory experiences. This review aims to highlight new findings in epigenetics research in C. elegans with the main focus on transgenerational epigenetic phenomena dependent on small RNAs.

由于其自我复制的基本过程,DNA 是大多数生物体繁殖和进化的核心。然而,它也编码了一些因子,这些因子允许表观遗传信息(不包括在 DNA 序列中)从亲代流向子代及更远的地方。已知的表观遗传机制包括 DNA 和染色质的化学修饰以及调控 RNA。所有这些因素都能调节后代的基因表达程序。线虫秀丽隐杆线虫(Caenorhabditis elegans)被认为是跨代表观遗传研究的先驱生物。秀丽隐杆线虫表观遗传学的最新进展包括:发现了限制基于 RNA 的表观遗传持续时间的控制机制、抵消表观遗传沉默建立的周期性 DNA 主题、对精子携带的表观遗传的新机理认识,以及感官经验遗传的诱人实例。这篇综述旨在重点介绍优雅小鼠表观遗传学研究的新发现,主要关注依赖于小 RNA 的跨代表观遗传现象。
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引用次数: 0
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DNA
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