Repetitive DNA sequences are abundant in the human genome and can adopt alternative (i.e., non-B) DNA structures. These sequences contribute to diverse biological functions, including genomic instability. Previously, we found that Z-DNA-, H-DNA- and cruciform DNA-forming sequences are mutagenic, implicating them in cancer etiology. These sequences can stimulate the formation of DNA double-strand breaks (DSBs), causing deletions via cleavage by the endonuclease ERCC1-XPF. Interestingly, the activity of ERCC1-XPF in H-DNA-induced mutagenesis is nucleotide excision repair (NER)-dependent, but its role in Z-DNA-induced mutagenesis is NER-independent. Instead, Z-DNA is processed by ERCC1-XPF in a mechanism dependent on the mismatch repair (MMR) complex, MSH2-MSH3. These observations indicate distinct mechanisms of non-B-induced genomic instability. However, the roles of NER and MMR proteins, as well as additional nucleases (CtIP and MRE11), in the processing of cruciform DNA remain unknown. Here, we present data on the processing of cruciform-forming short inverted repeats (IRs) by DNA repair proteins using mammalian cell-based systems. From this pilot study, we show that, in contrast to H-DNA and Z-DNA, short IRs are processed in a NER- and MMR-independent manner, and the nucleases CtIP and MRE11 suppress short IR-induced genomic instability in mammalian cells.
重复 DNA 序列在人类基因组中非常丰富，可采用替代性（即非 B 型）DNA 结构。这些序列具有多种生物功能，包括基因组不稳定性。此前，我们发现 Z-DNA、H-DNA 和十字形 DNA 形成序列具有致突变性，与癌症病因有关。这些序列可刺激 DNA 双链断裂（DSB）的形成，通过内切酶 ERCC1-XPF 的裂解造成缺失。有趣的是，ERCC1-XPF 在 H-DNA 诱导突变中的活性依赖核苷酸切除修复（NER），但在 Z-DNA 诱导突变中的作用却不依赖 NER。相反，ERCC1-XPF处理Z-DNA的机制依赖于错配修复（MMR）复合物MSH2-MSH3。这些观察结果表明了非 B 诱导的基因组不稳定性的不同机制。然而，NER 和 MMR 蛋白以及其他核酸酶（CtIP 和 MRE11）在十字形 DNA 处理过程中的作用仍然未知。在这里，我们利用基于哺乳动物细胞的系统，展示了 DNA 修复蛋白处理十字形短倒位重复序列（IR）的数据。通过这项试验性研究，我们发现与 H-DNA 和 Z-DNA 不同，短 IR 是以不依赖于 NER 和 MMR 的方式处理的，而核酸酶 CtIP 和 MRE11 能抑制哺乳动物细胞中短 IR 诱导的基因组不稳定性。
{"title":"Exploring the Roles of Different DNA Repair Proteins in Short Inverted Repeat Mediated Genomic Instability: A Pilot Study","authors":"Pooja Mandke, Karen M. Vasquez","doi":"10.3390/dna4020008","DOIUrl":"https://doi.org/10.3390/dna4020008","url":null,"abstract":"Repetitive DNA sequences are abundant in the human genome and can adopt alternative (i.e., non-B) DNA structures. These sequences contribute to diverse biological functions, including genomic instability. Previously, we found that Z-DNA-, H-DNA- and cruciform DNA-forming sequences are mutagenic, implicating them in cancer etiology. These sequences can stimulate the formation of DNA double-strand breaks (DSBs), causing deletions via cleavage by the endonuclease ERCC1-XPF. Interestingly, the activity of ERCC1-XPF in H-DNA-induced mutagenesis is nucleotide excision repair (NER)-dependent, but its role in Z-DNA-induced mutagenesis is NER-independent. Instead, Z-DNA is processed by ERCC1-XPF in a mechanism dependent on the mismatch repair (MMR) complex, MSH2-MSH3. These observations indicate distinct mechanisms of non-B-induced genomic instability. However, the roles of NER and MMR proteins, as well as additional nucleases (CtIP and MRE11), in the processing of cruciform DNA remain unknown. Here, we present data on the processing of cruciform-forming short inverted repeats (IRs) by DNA repair proteins using mammalian cell-based systems. From this pilot study, we show that, in contrast to H-DNA and Z-DNA, short IRs are processed in a NER- and MMR-independent manner, and the nucleases CtIP and MRE11 suppress short IR-induced genomic instability in mammalian cells.","PeriodicalId":72835,"journal":{"name":"DNA","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140738358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Since the discovery of transposable elements (TEs) in maize in the 1940s by Barbara McClintock transposable elements have been described as junk, as selfish elements with no benefit to the host, and more recently as major determinants of genome structure and genome evolution. TEs are DNA sequences that are capable of moving to new sites in the genome and making additional copies of themselves while doing so. To limit the propagation of TEs, host silencing mechanisms are directed at transposon-encoded genes that are required for mobilization. The mutagenic properties of TEs, the potential of TEs to form new genes and affect gene expression, together with the host silencing mechanisms, shape eukaryotic genomes and drive genome evolution. While TEs constitute more than half of the genome in many higher eukaryotes, transposable elements in the nematode C. elegans form a relatively small proportion of the genome (approximately 15%). Genetic studies of transposon silencing, and the discovery of RNA interference (RNAi) in C. elegans, propelled Caenorhabditis elegans (C. elegans) to the forefront of studies of RNA-based mechanisms that silence TEs. Here, I will review the transposable elements that are present and active in the C. elegans genome, and the host defense mechanisms that silence these elements.
自 20 世纪 40 年代芭芭拉-麦克林托克（Barbara McClintock）在玉米中发现可转座元件（Transposable elements，TEs）以来，可转座元件一直被描述为垃圾元件、对宿主无益的自私元件，最近则被描述为基因组结构和基因组进化的主要决定因素。转座元件是一种 DNA 序列，能够在基因组中移动到新的位点，并在移动的同时复制自己。为了限制 TE 的传播，宿主沉默机制针对的是转座子编码的基因，这些基因是转座子移动所必需的。转座因子的诱变特性、转座因子形成新基因和影响基因表达的潜力以及宿主沉默机制共同塑造了真核生物基因组，并推动了基因组进化。在许多高等真核生物中，TE 占基因组的一半以上，而在线虫秀丽隐杆线虫中，转座元件只占基因组相对较小的比例（约 15%）。对转座子沉默的遗传学研究以及 RNA 干扰（RNAi）在秀丽隐杆线虫中的发现，将秀丽隐杆线虫（C. elegans）推向了基于 RNA 的 TE 沉默机制研究的前沿。在这里，我将回顾一下在秀丽隐杆线虫基因组中存在和活跃的转座元件，以及使这些元件沉默的宿主防御机制。
{"title":"Activity and Silencing of Transposable Elements in C. elegans","authors":"Sylvia E. J. Fischer","doi":"10.3390/dna4020007","DOIUrl":"https://doi.org/10.3390/dna4020007","url":null,"abstract":"Since the discovery of transposable elements (TEs) in maize in the 1940s by Barbara McClintock transposable elements have been described as junk, as selfish elements with no benefit to the host, and more recently as major determinants of genome structure and genome evolution. TEs are DNA sequences that are capable of moving to new sites in the genome and making additional copies of themselves while doing so. To limit the propagation of TEs, host silencing mechanisms are directed at transposon-encoded genes that are required for mobilization. The mutagenic properties of TEs, the potential of TEs to form new genes and affect gene expression, together with the host silencing mechanisms, shape eukaryotic genomes and drive genome evolution. While TEs constitute more than half of the genome in many higher eukaryotes, transposable elements in the nematode C. elegans form a relatively small proportion of the genome (approximately 15%). Genetic studies of transposon silencing, and the discovery of RNA interference (RNAi) in C. elegans, propelled Caenorhabditis elegans (C. elegans) to the forefront of studies of RNA-based mechanisms that silence TEs. Here, I will review the transposable elements that are present and active in the C. elegans genome, and the host defense mechanisms that silence these elements.","PeriodicalId":72835,"journal":{"name":"DNA","volume":"203 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140751207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chromatin is the complex of DNA and associated proteins found in the nuclei of living organisms. How it is organized is a major research field as it has implications for replication, repair, and gene expression. This review summarizes the current state of the chromatin organization field, with a special focus on chromatin motor complexes cohesin and condensin. Containing the highly conserved SMC proteins, these complexes are responsible for organizing chromatin during cell division. Additionally, research has demonstrated that condensin and cohesin also have important functions during interphase to shape the organization of chromatin and regulate expression of genes. Using the model organism C. elegans, the authors review the current knowledge of how these complexes perform such diverse roles and what open questions still exist in the field.
染色质是生物体细胞核中的 DNA 和相关蛋白质的复合体。染色质如何组织是一个重要的研究领域，因为它对复制、修复和基因表达都有影响。这篇综述总结了染色质组织领域的现状，特别关注染色质运动复合物凝聚素和凝集素。这些复合体包含高度保守的 SMC 蛋白，负责在细胞分裂过程中组织染色质。此外，研究表明，凝集素和凝聚素在细胞间期也具有重要功能，可塑造染色质的组织结构并调控基因的表达。作者以模式生物 elegans 为例，回顾了这些复合体如何发挥如此多样作用的现有知识，以及该领域还存在哪些未决问题。
{"title":"How Chromatin Motor Complexes Influence the Nuclear Architecture: A Review of Chromatin Organization, Cohesins, and Condensins with a Focus on C. elegans","authors":"Bahaar Chawla, G. Csankovszki","doi":"10.3390/dna4010005","DOIUrl":"https://doi.org/10.3390/dna4010005","url":null,"abstract":"Chromatin is the complex of DNA and associated proteins found in the nuclei of living organisms. How it is organized is a major research field as it has implications for replication, repair, and gene expression. This review summarizes the current state of the chromatin organization field, with a special focus on chromatin motor complexes cohesin and condensin. Containing the highly conserved SMC proteins, these complexes are responsible for organizing chromatin during cell division. Additionally, research has demonstrated that condensin and cohesin also have important functions during interphase to shape the organization of chromatin and regulate expression of genes. Using the model organism C. elegans, the authors review the current knowledge of how these complexes perform such diverse roles and what open questions still exist in the field.","PeriodicalId":72835,"journal":{"name":"DNA","volume":"40 11‐12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140252258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Embryogenesis is characterized by dynamic chromatin remodeling and broad changes in chromosome architecture. These changes in chromatin organization are accompanied by transcriptional changes, which are crucial for the proper development of the embryo. Several independent mechanisms regulate this process of chromatin reorganization, including the segregation of chromatin into heterochromatin and euchromatin, deposition of active and repressive histone modifications, and the formation of 3D chromatin domains such as TADs and LADs. These changes in chromatin structure are directly linked to developmental milestones such as the loss of developmental plasticity and acquisition of terminally differentiated cell identities. In this review, we summarize these processes that underlie this chromatin reorganization and their impact on embryogenesis in the nematode C. elegans.
胚胎发生的特点是动态染色质重塑和染色体结构的广泛变化。染色质组织的这些变化伴随着转录变化，而转录变化对胚胎的正常发育至关重要。染色质重组过程受多种独立机制的调控，包括染色质在异染色质和真染色质中的分离、活性和抑制性组蛋白修饰的沉积以及三维染色质域（如 TAD 和 LAD）的形成。染色质结构的这些变化与发育里程碑直接相关，如发育可塑性的丧失和终末分化细胞特性的获得。在这篇综述中，我们将总结这些染色质重组的过程及其对线虫C. elegans胚胎发生的影响。
{"title":"Chromatin Organization during C. elegans Early Development","authors":"Eshna Jash, G. Csankovszki","doi":"10.3390/dna4010004","DOIUrl":"https://doi.org/10.3390/dna4010004","url":null,"abstract":"Embryogenesis is characterized by dynamic chromatin remodeling and broad changes in chromosome architecture. These changes in chromatin organization are accompanied by transcriptional changes, which are crucial for the proper development of the embryo. Several independent mechanisms regulate this process of chromatin reorganization, including the segregation of chromatin into heterochromatin and euchromatin, deposition of active and repressive histone modifications, and the formation of 3D chromatin domains such as TADs and LADs. These changes in chromatin structure are directly linked to developmental milestones such as the loss of developmental plasticity and acquisition of terminally differentiated cell identities. In this review, we summarize these processes that underlie this chromatin reorganization and their impact on embryogenesis in the nematode C. elegans.","PeriodicalId":72835,"journal":{"name":"DNA","volume":"28 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140439642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Eszter É. Lőrincz, Norbert Mátrai, Katalin A. Rádóczy, Tamás Cseppentő, Nóra M. Magonyi, Attila Heinrich
The PowerPlex Fusion 6C PCR™ amplification kit provides a strong discriminatory power for human identification. We have validated the kit with a reduced volume (12.5 µL) and as part of the validation we compared the efficiency of the polymerase chain reaction (PCR) prepared manually and on Hamilton Microlab® Autolys STAR Biorobot. Three years of casework data has been also included in the validation. Optimisation was carried out on different types of samples (blood, saliva, semen) and DNA was extracted robotically. Tests were conducted at two different cycle numbers (30;32), followed by analysis on both the Applied BiosystemsTM 3500 and 3500 xL Genetic Analyzer instruments (Applied Biosystems®, Foster City, CA, USA). When the PCR was prepared manually, no allele dropout was observed over 0.15 ng input DNA. Whereas when the PCR was prepared robotically, dropout already appeared at the level of 0.15 ng input DNA. In cases when increased cycle number was utilised, an increasing number of dropouts started to arise from 0.075 ng total input DNA. Despite the fact that robotically prepared PCR produced more missing alleles than the manually prepared PCR, using the optimal 0.5 ng input DNA, both methods proved to be reliable. Based on the results, our half-volume protocol is robust, and after three years of application it has proven to be effective with respect to a large number of casework samples.
PowerPlex Fusion 6C PCR™ 扩增试剂盒具有很强的人体识别鉴别能力。我们已对该试剂盒进行了验证，试剂盒的容量有所减少（12.5 µL），作为验证的一部分，我们比较了手动和 Hamilton Microlab® Autolys STAR Biorobot 上聚合酶链反应 (PCR) 的效率。验证还包括三年的案例工作数据。对不同类型的样本（血液、唾液、精液）进行了优化，并使用机器人提取 DNA。测试在两个不同的周期数（30；32）下进行，然后在应用生物系统 3500 和 3500 xL 基因分析仪（Applied Biosystems®, Foster City, CA, USA）上进行分析。手工制备 PCR 时，输入的 DNA 超过 0.15 纳克就不会出现等位基因丢失。而用机器人进行 PCR 时，在 0.15 纳克输入 DNA 的水平上就已经出现了等位基因丢失。当循环次数增加时，从 0.075 纳克总输入 DNA 开始出现越来越多的脱落。尽管在使用最佳 0.5 纳克输入 DNA 时，机器人 PCR 比人工 PCR 产生更多的等位基因缺失，但两种方法都证明是可靠的。根据这些结果，我们的半体积方案是可靠的，经过三年的应用，它已被证明对大量的个案样本是有效的。
{"title":"Comparison of Reduced PCR Volume PowerPlex Fusion 6C Kit Validations on Manual and Automated Systems","authors":"Eszter É. Lőrincz, Norbert Mátrai, Katalin A. Rádóczy, Tamás Cseppentő, Nóra M. Magonyi, Attila Heinrich","doi":"10.3390/dna4010003","DOIUrl":"https://doi.org/10.3390/dna4010003","url":null,"abstract":"The PowerPlex Fusion 6C PCR™ amplification kit provides a strong discriminatory power for human identification. We have validated the kit with a reduced volume (12.5 µL) and as part of the validation we compared the efficiency of the polymerase chain reaction (PCR) prepared manually and on Hamilton Microlab® Autolys STAR Biorobot. Three years of casework data has been also included in the validation. Optimisation was carried out on different types of samples (blood, saliva, semen) and DNA was extracted robotically. Tests were conducted at two different cycle numbers (30;32), followed by analysis on both the Applied BiosystemsTM 3500 and 3500 xL Genetic Analyzer instruments (Applied Biosystems®, Foster City, CA, USA). When the PCR was prepared manually, no allele dropout was observed over 0.15 ng input DNA. Whereas when the PCR was prepared robotically, dropout already appeared at the level of 0.15 ng input DNA. In cases when increased cycle number was utilised, an increasing number of dropouts started to arise from 0.075 ng total input DNA. Despite the fact that robotically prepared PCR produced more missing alleles than the manually prepared PCR, using the optimal 0.5 ng input DNA, both methods proved to be reliable. Based on the results, our half-volume protocol is robust, and after three years of application it has proven to be effective with respect to a large number of casework samples.","PeriodicalId":72835,"journal":{"name":"DNA","volume":"2015 33","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139807155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Eszter É. Lőrincz, Norbert Mátrai, Katalin A. Rádóczy, Tamás Cseppentő, Nóra M. Magonyi, Attila Heinrich
The PowerPlex Fusion 6C PCR™ amplification kit provides a strong discriminatory power for human identification. We have validated the kit with a reduced volume (12.5 µL) and as part of the validation we compared the efficiency of the polymerase chain reaction (PCR) prepared manually and on Hamilton Microlab® Autolys STAR Biorobot. Three years of casework data has been also included in the validation. Optimisation was carried out on different types of samples (blood, saliva, semen) and DNA was extracted robotically. Tests were conducted at two different cycle numbers (30;32), followed by analysis on both the Applied BiosystemsTM 3500 and 3500 xL Genetic Analyzer instruments (Applied Biosystems®, Foster City, CA, USA). When the PCR was prepared manually, no allele dropout was observed over 0.15 ng input DNA. Whereas when the PCR was prepared robotically, dropout already appeared at the level of 0.15 ng input DNA. In cases when increased cycle number was utilised, an increasing number of dropouts started to arise from 0.075 ng total input DNA. Despite the fact that robotically prepared PCR produced more missing alleles than the manually prepared PCR, using the optimal 0.5 ng input DNA, both methods proved to be reliable. Based on the results, our half-volume protocol is robust, and after three years of application it has proven to be effective with respect to a large number of casework samples.
PowerPlex Fusion 6C PCR™ 扩增试剂盒具有很强的人体识别鉴别能力。我们已对该试剂盒进行了验证，试剂盒的容量有所减少（12.5 µL），作为验证的一部分，我们比较了手动和 Hamilton Microlab® Autolys STAR Biorobot 上聚合酶链反应 (PCR) 的效率。验证还包括三年的案例工作数据。对不同类型的样本（血液、唾液、精液）进行了优化，并使用机器人提取 DNA。测试在两个不同的周期数（30；32）下进行，然后在应用生物系统 3500 和 3500 xL 基因分析仪（Applied Biosystems®, Foster City, CA, USA）上进行分析。手工制备 PCR 时，输入的 DNA 超过 0.15 纳克就不会出现等位基因丢失。而用机器人进行 PCR 时，在 0.15 纳克输入 DNA 的水平上就已经出现了等位基因丢失。当循环次数增加时，从 0.075 纳克总输入 DNA 开始出现越来越多的脱落。尽管在使用最佳 0.5 纳克输入 DNA 时，机器人 PCR 比人工 PCR 产生更多的等位基因缺失，但两种方法都证明是可靠的。根据这些结果，我们的半体积方案是可靠的，经过三年的应用，它已被证明对大量的个案样本是有效的。
{"title":"Comparison of Reduced PCR Volume PowerPlex Fusion 6C Kit Validations on Manual and Automated Systems","authors":"Eszter É. Lőrincz, Norbert Mátrai, Katalin A. Rádóczy, Tamás Cseppentő, Nóra M. Magonyi, Attila Heinrich","doi":"10.3390/dna4010003","DOIUrl":"https://doi.org/10.3390/dna4010003","url":null,"abstract":"The PowerPlex Fusion 6C PCR™ amplification kit provides a strong discriminatory power for human identification. We have validated the kit with a reduced volume (12.5 µL) and as part of the validation we compared the efficiency of the polymerase chain reaction (PCR) prepared manually and on Hamilton Microlab® Autolys STAR Biorobot. Three years of casework data has been also included in the validation. Optimisation was carried out on different types of samples (blood, saliva, semen) and DNA was extracted robotically. Tests were conducted at two different cycle numbers (30;32), followed by analysis on both the Applied BiosystemsTM 3500 and 3500 xL Genetic Analyzer instruments (Applied Biosystems®, Foster City, CA, USA). When the PCR was prepared manually, no allele dropout was observed over 0.15 ng input DNA. Whereas when the PCR was prepared robotically, dropout already appeared at the level of 0.15 ng input DNA. In cases when increased cycle number was utilised, an increasing number of dropouts started to arise from 0.075 ng total input DNA. Despite the fact that robotically prepared PCR produced more missing alleles than the manually prepared PCR, using the optimal 0.5 ng input DNA, both methods proved to be reliable. Based on the results, our half-volume protocol is robust, and after three years of application it has proven to be effective with respect to a large number of casework samples.","PeriodicalId":72835,"journal":{"name":"DNA","volume":"19 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139866998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Motivation: Clustered DNA-lesions are predominantly induced by ionizing radiation, particularly by high-LET particles, and considered as lethal damage. Quantification of this specific type of damage as a function of radiation parameters such as LET, dose rate, dose, and particle type can be informative for the prediction of biological outcome in radiobiological studies. This study investigated the induction and complexity of clustered DNA damage for three different types of particles at an LET range of 0.5–250 keV/µm. Methods: Nanometric volumes (36.0 nm3) of 15 base-pair DNA with its hydration shell was modeled. Electron, proton, and alpha particles at various energies were simulated to irradiate the nanometric volumes. The number of ionization events, low-energy electron spectra, and chemical yields for the formation of °OH, H°, eaq−, and H2O2 were calculated for each particle as a function of LET. Single- and double-strand breaks (SSB and DSB), base release, and clustered DNA-lesions were computed from the Monte-Carlo based quantification of the reactive species and measured yields of the species responsible for the DNA lesion formation. Results: The total amount of DNA damage depends on particle type and LET. The number of ionization events underestimates the quantity of DNA damage at LETs higher than 10 keV/µm. Minimum LETs of 9.4 and 11.5 keV/µm are required to induce clustered damage by a single track of proton and alpha particles, respectively. For a given radiation dose, an increase in LET reduces the number of particle tracks, leading to more complex clustered DNA damage, but a smaller number of separated clustered damage sites. Conclusions: The dependency of the number and the complexity of clustered DNA damage on LET and fluence suggests that the quantification of this damage can be a useful method for the estimation of the biological effectiveness of radiation. These results also suggest that medium-LET particles are more appropriate for the treatment of bulk targets, whereas high-LET particles can be more effective for small targets.
动机成簇的 DNA 分裂主要由电离辐射，尤其是高 LET 粒子诱发，被认为是致命的损伤。将这种特定类型的损伤量化为辐射参数（如 LET、剂量率、剂量和粒子类型）的函数，可为放射生物学研究中生物结果的预测提供信息。本研究调查了在 0.5-250 keV/µm 的 LET 范围内，三种不同类型粒子诱导的成簇 DNA 损伤及其复杂性。研究方法对 15 个碱基对 DNA 及其水合外壳的纳米体积（36.0 nm3）进行建模。模拟了不同能量的电子、质子和阿尔法粒子对纳米体积的照射。计算了每种粒子的电离事件数、低能电子能谱以及形成 °OH、H°、eaq- 和 H2O2 的化学产率与 LET 的函数关系。单链和双链断裂（SSB 和 DSB）、碱基释放和簇状 DNA 病变是根据蒙特卡洛反应物的定量和 DNA 病变形成的反应物的测量产率计算得出的。结果显示DNA 损伤的总量取决于粒子类型和 LET。当 LET 超过 10 keV/µm 时，电离事件的数量低估了 DNA 损伤的数量。质子和阿尔法粒子的单一轨道分别需要 9.4 和 11.5 keV/µm 的最小 LET 才能诱发成簇的损伤。在给定的辐射剂量下，LET 的增加会减少粒子轨迹的数量，从而导致更复杂的成簇 DNA 损伤，但分离的成簇损伤位点的数量会减少。结论成簇 DNA 损伤的数量和复杂程度与 LET 和通量的关系表明，对这种损伤进行量化是估算辐射生物有效性的一种有用方法。这些结果还表明，中等 LET 粒子更适合处理大块目标，而高 LET 粒子对小目标更有效。
{"title":"The Effects of Particle LET and Fluence on the Complexity and Frequency of Clustered DNA Damage","authors":"M. Rezaee, A. Adhikary","doi":"10.3390/dna4010002","DOIUrl":"https://doi.org/10.3390/dna4010002","url":null,"abstract":"Motivation: Clustered DNA-lesions are predominantly induced by ionizing radiation, particularly by high-LET particles, and considered as lethal damage. Quantification of this specific type of damage as a function of radiation parameters such as LET, dose rate, dose, and particle type can be informative for the prediction of biological outcome in radiobiological studies. This study investigated the induction and complexity of clustered DNA damage for three different types of particles at an LET range of 0.5–250 keV/µm. Methods: Nanometric volumes (36.0 nm3) of 15 base-pair DNA with its hydration shell was modeled. Electron, proton, and alpha particles at various energies were simulated to irradiate the nanometric volumes. The number of ionization events, low-energy electron spectra, and chemical yields for the formation of °OH, H°, eaq−, and H2O2 were calculated for each particle as a function of LET. Single- and double-strand breaks (SSB and DSB), base release, and clustered DNA-lesions were computed from the Monte-Carlo based quantification of the reactive species and measured yields of the species responsible for the DNA lesion formation. Results: The total amount of DNA damage depends on particle type and LET. The number of ionization events underestimates the quantity of DNA damage at LETs higher than 10 keV/µm. Minimum LETs of 9.4 and 11.5 keV/µm are required to induce clustered damage by a single track of proton and alpha particles, respectively. For a given radiation dose, an increase in LET reduces the number of particle tracks, leading to more complex clustered DNA damage, but a smaller number of separated clustered damage sites. Conclusions: The dependency of the number and the complexity of clustered DNA damage on LET and fluence suggests that the quantification of this damage can be a useful method for the estimation of the biological effectiveness of radiation. These results also suggest that medium-LET particles are more appropriate for the treatment of bulk targets, whereas high-LET particles can be more effective for small targets.","PeriodicalId":72835,"journal":{"name":"DNA","volume":"34 41","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139382671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Carol A. Stepien, Haila K. Schultz, Sean M. McAllister, Emily L. Norton, J. Keister
Zooplankton and ichthyoplankton community assessments depend on species diagnostics, yet morphological identifications are time-consuming, require taxonomic expertise, and are hampered by a lack of diagnostic characters, particularly for larval stages. Metabarcoding can identify multiple species in communities from short DNA sequences in comparison to reference databases. To evaluate species resolution across phylogenetic groups and food webs of zooplankton and ichthyoplankton, we compare five metabarcode mitochondrial (mt)DNA markers from gene regions of (a) cytochrome c oxidase subunit I, (b) cytochrome b, (c) 16S ribosomal RNA, and (d) 12S ribosomal RNA for DNA extracted from net tows in the Northeastern Pacific Ocean’s Salish Sea across seven sites and two seasons. Species resolved by metabarcoding are compared to invertebrate morphological identifications and biomass estimates. Results indicate that species resolution for different zooplankton and ichthyoplankton taxa can markedly vary among gene regions and markers in comparison to morphological identifications. Thus, researchers seeking “universal” metabarcoding should take caution that several markers and gene regions likely will be needed; all will miss some taxa and yield incomplete overlap. Species resolution requires careful attention to taxon marker selection and coverage in reference sequence repositories. In summary, combined multi-marker metabarcoding and morphological approaches improve broadscale zooplankton diagnostics.
浮游动物和鱼类浮游生物群落评估依赖于物种诊断，但形态学鉴定耗时长，需要分类学专业知识，并且因缺乏诊断特征（尤其是幼虫阶段）而受到阻碍。与参考数据库相比，元条码可通过短 DNA 序列识别群落中的多个物种。为了评估浮游动物和鱼类浮游生物在系统发生群和食物网中的物种分辨率，我们比较了从东北太平洋咸海七个地点和两个季节的网拖中提取的 DNA 的五个元条码线粒体（mt）DNA 标记：(a) 细胞色素 c 氧化酶亚单位 I、(b) 细胞色素 b、(c) 16S 核糖体 RNA 和 (d) 12S 核糖体 RNA。通过元条码解析的物种与无脊椎动物形态鉴定和生物量估计进行了比较。结果表明，与形态鉴定相比，不同浮游动物和鱼类类群的物种分辨率在基因区域和标记之间会有明显差异。因此，寻求 "通用 "代谢编码的研究人员应注意，可能需要多个标记物和基因区域；所有标记物和基因区域都会遗漏某些类群，并产生不完全的重叠。物种解析需要仔细关注分类群标记的选择和参考序列库的覆盖范围。总之，将多标记元标码和形态学方法结合起来可提高浮游动物的广泛诊断能力。
{"title":"Evaluating Metabarcoding Markers for Identifying Zooplankton and Ichthyoplankton Communities to Species in the Salish Sea: Morphological Comparisons and Rare, Threatened or Invasive Species","authors":"Carol A. Stepien, Haila K. Schultz, Sean M. McAllister, Emily L. Norton, J. Keister","doi":"10.3390/dna4010001","DOIUrl":"https://doi.org/10.3390/dna4010001","url":null,"abstract":"Zooplankton and ichthyoplankton community assessments depend on species diagnostics, yet morphological identifications are time-consuming, require taxonomic expertise, and are hampered by a lack of diagnostic characters, particularly for larval stages. Metabarcoding can identify multiple species in communities from short DNA sequences in comparison to reference databases. To evaluate species resolution across phylogenetic groups and food webs of zooplankton and ichthyoplankton, we compare five metabarcode mitochondrial (mt)DNA markers from gene regions of (a) cytochrome c oxidase subunit I, (b) cytochrome b, (c) 16S ribosomal RNA, and (d) 12S ribosomal RNA for DNA extracted from net tows in the Northeastern Pacific Ocean’s Salish Sea across seven sites and two seasons. Species resolved by metabarcoding are compared to invertebrate morphological identifications and biomass estimates. Results indicate that species resolution for different zooplankton and ichthyoplankton taxa can markedly vary among gene regions and markers in comparison to morphological identifications. Thus, researchers seeking “universal” metabarcoding should take caution that several markers and gene regions likely will be needed; all will miss some taxa and yield incomplete overlap. Species resolution requires careful attention to taxon marker selection and coverage in reference sequence repositories. In summary, combined multi-marker metabarcoding and morphological approaches improve broadscale zooplankton diagnostics.","PeriodicalId":72835,"journal":{"name":"DNA","volume":"42 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138945633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Joelson Germano Crispim, Elenilson dos Santos Souza, Marina Ferreira Kitazono Antunes, Hai Liu, Valesca Pandolfi, Marciana Bizerra de Morais, Lili Sun, Cláudia Ulisses, Roel Collamat Rabara, José Ribamar Costa Ferreira-Neto, Ana Maria Benko-Iseppon, Michael P. Timko, Ana Christina Brasileiro-Vidal
WRKY transcription factors play a pivotal role in regulating stress signaling pathways, including those associated with salt stress response. The present work characterized the effects of two WRKY genes from Vigna unguiculata, namely VuWRKY21 and VuWRKY87, on enhancing plant salinity tolerance. Under salt stress conditions, Arabidopsis lines expressing VuWRKY21 or VuWRKY87 showed elevated expression of genes participating in saline stress response pathways and reduced oxidative stress induced by reactive oxygen species (ROS). Among the salt-responsive genes in Arabidopsis, AtP5CS1, AtNHX1, AtRD29A, AtSOS3, AtSOS2, and AtSOS1 exhibited modulated expression levels after stress imposition. Furthermore, compared to wild-type plants, at most evaluated times, transgenic lines, on average, presented lower H2O2 content while displaying higher content of SOD (EC: 1.15.1.1) and CAT (EC: 1.11.1.6) at early stages of salt stress. These findings suggest that the expression of both VuWRKY genes in Arabidopsis, particularly VuWRKY21, activated genes involved in salinity tolerance.
{"title":"Expression of Cowpea VuWRKY21 and VuWRKY87 Genes in Arabidopsis thaliana Confers Plant Tolerance to Salt Stress","authors":"Joelson Germano Crispim, Elenilson dos Santos Souza, Marina Ferreira Kitazono Antunes, Hai Liu, Valesca Pandolfi, Marciana Bizerra de Morais, Lili Sun, Cláudia Ulisses, Roel Collamat Rabara, José Ribamar Costa Ferreira-Neto, Ana Maria Benko-Iseppon, Michael P. Timko, Ana Christina Brasileiro-Vidal","doi":"10.3390/dna3040014","DOIUrl":"https://doi.org/10.3390/dna3040014","url":null,"abstract":"WRKY transcription factors play a pivotal role in regulating stress signaling pathways, including those associated with salt stress response. The present work characterized the effects of two WRKY genes from Vigna unguiculata, namely VuWRKY21 and VuWRKY87, on enhancing plant salinity tolerance. Under salt stress conditions, Arabidopsis lines expressing VuWRKY21 or VuWRKY87 showed elevated expression of genes participating in saline stress response pathways and reduced oxidative stress induced by reactive oxygen species (ROS). Among the salt-responsive genes in Arabidopsis, AtP5CS1, AtNHX1, AtRD29A, AtSOS3, AtSOS2, and AtSOS1 exhibited modulated expression levels after stress imposition. Furthermore, compared to wild-type plants, at most evaluated times, transgenic lines, on average, presented lower H2O2 content while displaying higher content of SOD (EC: 1.15.1.1) and CAT (EC: 1.11.1.6) at early stages of salt stress. These findings suggest that the expression of both VuWRKY genes in Arabidopsis, particularly VuWRKY21, activated genes involved in salinity tolerance.","PeriodicalId":72835,"journal":{"name":"DNA","volume":"21 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135391215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Teratozoospermia, a complex male fertility disorder affecting sperm morphology, has been linked to AURKC, SPATA16, and SUN5 gene defects. However, the sheer volume of SNPs in these genes necessitates prioritization for comprehensive analysis. This study focuses on the often-overlooked untranslated region (UTR) variants in these genes, aiming to assess their association with teratozoospermia and prioritize them. We employed a multi-step filtering process, including functional significance assessment (RegulomeDB, 3DSNP v2.0, SNPinfo (FuncPred)), evaluation of gene expression impacts in testis tissue using GTEx, and assessment of miRNA binding site effects (PolymiRTS Database 3.0, miRNASNP v3). Additionally, we used SNPnexus to evaluate their conservation and association with diseases. In AURKC, we identified six UTR SNPs (rs11084490, rs58264281, rs35582299, rs533889458, rs2361127, rs55710619), two of which influenced gene expression in testis, while others affected the binding sites of 29 miRNAs or were located in transcription-factor binding sites. Three of these SNPs were also found to be associated with spermatogenic failure according to previous studies indicating a potential regulatory role in teratozoospermia, too. For SPATA16, two 3′ UTR variants, rs146640459 and rs148085657, were prioritized, with the latter impacting miRNA binding sites. In SUN5, three 3′ UTR variants (rs1485087675, rs762026146, rs1478197315) affected miRNA binding sites. It should be noted that none of the above variants was identified in a conserved region. Our findings shed light on the potential regulatory roles of these SNPs in teratozoospermia and lay the foundation for future research directions in this area.
{"title":"Genetic Insights into Teratozoospermia: A Comprehensive Computational Study of UTR Variants in AURKC, SPATA16, and SUN5","authors":"Maria-Anna Kyrgiafini, Zissis Mamuris","doi":"10.3390/dna3040013","DOIUrl":"https://doi.org/10.3390/dna3040013","url":null,"abstract":"Teratozoospermia, a complex male fertility disorder affecting sperm morphology, has been linked to AURKC, SPATA16, and SUN5 gene defects. However, the sheer volume of SNPs in these genes necessitates prioritization for comprehensive analysis. This study focuses on the often-overlooked untranslated region (UTR) variants in these genes, aiming to assess their association with teratozoospermia and prioritize them. We employed a multi-step filtering process, including functional significance assessment (RegulomeDB, 3DSNP v2.0, SNPinfo (FuncPred)), evaluation of gene expression impacts in testis tissue using GTEx, and assessment of miRNA binding site effects (PolymiRTS Database 3.0, miRNASNP v3). Additionally, we used SNPnexus to evaluate their conservation and association with diseases. In AURKC, we identified six UTR SNPs (rs11084490, rs58264281, rs35582299, rs533889458, rs2361127, rs55710619), two of which influenced gene expression in testis, while others affected the binding sites of 29 miRNAs or were located in transcription-factor binding sites. Three of these SNPs were also found to be associated with spermatogenic failure according to previous studies indicating a potential regulatory role in teratozoospermia, too. For SPATA16, two 3′ UTR variants, rs146640459 and rs148085657, were prioritized, with the latter impacting miRNA binding sites. In SUN5, three 3′ UTR variants (rs1485087675, rs762026146, rs1478197315) affected miRNA binding sites. It should be noted that none of the above variants was identified in a conserved region. Our findings shed light on the potential regulatory roles of these SNPs in teratozoospermia and lay the foundation for future research directions in this area.","PeriodicalId":72835,"journal":{"name":"DNA","volume":"42 8-9","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134908664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：