IF 3 3区生物学

DNA Repair Pub Date : 2025-06-01 DOI: 10.1016/j.dnarep.2025.103852

Giovannia M. Barbosa, Sarah Delaney

{"title":"Initiation of base excision repair is modulated by nucleosome occupancy modifying sequences","authors":"Giovannia M. Barbosa, Sarah Delaney","doi":"10.1016/j.dnarep.2025.103852","DOIUrl":"10.1016/j.dnarep.2025.103852","url":null,"abstract":"<div><div>Nucleosome occupancy varies across the genome and plays a critical role in modulating DNA accessibility. While the effect of occupancy on gene expression has been studied, its influence on DNA repair, particularly base excision repair (BER), remains unexplored. In this work, we investigate the relationship between nucleosome occupancy and the initiation of BER by reconstituting nucleosome core particles (NCPs) using four DNA sequences known to modulate nucleosome occupancy <em>in vivo</em>. The results demonstrate that histone-DNA interactions differ significantly among these sequences. Moreover, uracil DNA glycosylase (UDG) activity is limited to solution-accessible uracil (U) lesion sites on NCPs containing the high occupancy sequences M4 and SB. In contrast, UDG displays high activity on NCPs containing the low occupancy sequences M2 and M3, even at less solution accessible lesion sites. In fact, for NCPs containing the sequence with the lowest occupancy, M2, UDG exhibits high activity regardless of the U lesion position. However, this high level of activity regardless of lesion position was not observed for thymine DNA glycosylase (TDG) and single-stranded monofunctional uracil DNA glycosylase 1 (SMUG1). Instead, the activity of TDG was dictated by the sequence flanking the U with a preference for 5′-UpG-3′ and 5′-UpA-3′ sequences, consistent with the role of TDG in epigenetic regulation. SMUG1 activity is high at many U sites but is severely hindered in the dyad region. These results highlight the interplay between nucleosome occupancy and BER, offering new insights into the dynamics of chromatin and DNA repair.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"150 ","pages":"Article 103852"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144177901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DNA polymerase beta expression in head & neck cancer modulates the poly(ADP-ribose)-mediated replication checkpoint DNA聚合酶β在头颈癌中的表达调节poly（adp -核糖）介导的复制检查点

IF 3 3区生物学

DNA Repair Pub Date : 2025-06-01 DOI: 10.1016/j.dnarep.2025.103853

Md Maruf Khan , Wynand P. Roos , Charlotte R. Pearson , Stefan M. Leonard , Anusha Angajala , Denise Y. Gibbs , Jeffrey C. Liu , Camille Ragin , Robert W. Sobol

{"title":"DNA polymerase beta expression in head & neck cancer modulates the poly(ADP-ribose)-mediated replication checkpoint","authors":"Md Maruf Khan , Wynand P. Roos , Charlotte R. Pearson , Stefan M. Leonard , Anusha Angajala , Denise Y. Gibbs , Jeffrey C. Liu , Camille Ragin , Robert W. Sobol","doi":"10.1016/j.dnarep.2025.103853","DOIUrl":"10.1016/j.dnarep.2025.103853","url":null,"abstract":"<div><div>Head and Neck Squamous Cell Carcinoma (HNSCC) imposes a significant health burden, necessitating innovative therapeutic strategies to enhance treatment efficacy. Current treatments, such as surgery, radiation, and chemotherapy, have limited effectiveness and yield severe side effects, emphasizing the need for targeted therapies. We have focused on DNA polymerase beta (Polβ) and its roles in replication stress, cellular responses to DNA damaging-therapies, and DNA damage response modifiers. Our investigations reveal a regulatory role for base excision repair (BER) proteins, including Polβ, in the cellular response to inhibitors of poly(ADP-ribose) glycohydrolase (PARG), an enzyme involved in poly(ADP-ribose) (PAR) degradation. The inhibition of PARG, in HNSCC cells, elicits replication stress and activates the PAR-induced S-phase/ATR checkpoint, leading to a block to replication, cell cycle arrest, and the onset of apoptosis. However, Polβ overexpression mitigates this response, reducing replication-stress-induced PAR foci formation, suggesting a modulation of replication checkpoint activation. We found that PARG inhibitor treatment is ineffective on HNSCC cells that overexpress Polβ, implying that the PARG inhibitor-induced PAR and apoptotic response is dependent on the level of Polβ. Further, our in vitro experiments demonstrate that combining PARG and ATR/CHK1 inhibitors overcomes Polβ-mediated treatment resistance in HNSCC cells, producing synergistic effects compared to the individual treatment conditions. Our findings suggest a possible treatment paradigm for HNSCC, employing ATR or CHK1 inhibitors in combination with PARG inhibitors. This strategy offers a promising path for more effective HNSCC treatments, potentially overcoming Polβ-related resistance.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"150 ","pages":"Article 103853"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144205275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dynamics of chromatin factors RSF1, CENPS and CENPX at DNA damage sites 染色质因子RSF1、CENPS和CENPX在DNA损伤位点的动态变化

IF 3 3区生物学

DNA Repair Pub Date : 2025-06-01 DOI: 10.1016/j.dnarep.2025.103850

Pritishkumar Tidke , Andrew Flaus , Helen Dodson

{"title":"Dynamics of chromatin factors RSF1, CENPS and CENPX at DNA damage sites","authors":"Pritishkumar Tidke , Andrew Flaus , Helen Dodson","doi":"10.1016/j.dnarep.2025.103850","DOIUrl":"10.1016/j.dnarep.2025.103850","url":null,"abstract":"<div><div>Chromatin has a major influence on the DNA damage response (DDR). Several chromatin-related factors participate in specialised DNA packaging during the DDR including the CENPS and CENPX histone fold proteins, also known as MHF1/2, and the chromatin remodelling factor RSF1 although their contribution has remained unclear. We defined a timeline for RSF1, CENPS, and CENPX recruitment at DNA double strand breaks (DSBs) induced in live HeLa cells by microirradiation and calibrated this to published data to clarify the potential for their involvement in the DDR. CENPS, CENPX and RSF1 are recruited with a half time of ∼100 s and removed with a half time of ∼2000 s. Enrichment for cell cycle phase revealed that this recruitment occurs in G1, S and G2 phases, but that its half time in G2 appears to be delayed and stronger than in G1. Integration of these observations with timelines for other DDR factors reveals that CENPS and CENPX recruitment occurs simultaneously immediately after ATM activation and RNF8-RNF168 activity. The removal of CENPS and CENPX is at a similar time to loading of RPA and assembly of RAD51. This places RSF1, CENPS and CENPX in the vicinity of DSBs at the time when nucleosomes are being actively remodelled during the chromatin-dependent early response to DNA damage involving pathway choice and resection, and their increased abundance at DSBs in G2 correlates with extended resection for HR.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"150 ","pages":"Article 103850"},"PeriodicalIF":3.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144189396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development and characterization of a novel NEIL1 nanobody 一种新型NEIL1纳米体的研制与表征

IF 3 3区生物学

DNA Repair Pub Date : 2025-05-22 DOI: 10.1016/j.dnarep.2025.103849

Marlo K. Thompson , Mark H. Eggers , Danielle Flores , Israel Valenzuela , Zhengrong Yang , Joel F. Andrews , Tom Johnsten , Aishwarya Prakash

{"title":"Development and characterization of a novel NEIL1 nanobody","authors":"Marlo K. Thompson , Mark H. Eggers , Danielle Flores , Israel Valenzuela , Zhengrong Yang , Joel F. Andrews , Tom Johnsten , Aishwarya Prakash","doi":"10.1016/j.dnarep.2025.103849","DOIUrl":"10.1016/j.dnarep.2025.103849","url":null,"abstract":"<div><div>Nei endonuclease VIII-like 1 (NEIL1) is a bifunctional human DNA glycosylase that catalyzes the first step of the base excision repair (BER) pathway by recognizing and excising oxidized bases, including thymine glycol and the further oxidation products of 7,8-dihydro-8-oxoguanine (8-oxoG), spiroiminodihydantoin, and guanidinohydantoin. Despite its critical role in maintaining genome stability, NEIL1 is expressed at relatively low endogenous cellular levels compared to other BER proteins such as OGG1, Polβ, and APE1. As a result, most cellular studies have relied on overexpression systems. Additionally, progress in studying NEIL1 has been hindered by the inconsistent availability and continuity of specific commercially available antibodies. To address this challenge, we developed single-domain nanobodies (VHHs) targeting NEIL1. A yeast 2 hybrid (Y2H) screen identified ten VHH hits with the top candidate, henceforth called A5, emerging multiple times. Here, we characterize the binding properties of A5 using a combination of biochemical and molecular techniques. Differential scanning fluorimetry and glycosylase activity assays indicate that recombinant A5 specifically stabilizes recombinantly expressed NEIL1, while not interfering with its glycosylase activity. Moreover, our data suggest that A5 preferentially binds to NEIL1’s N-terminal glycosylase domain rather than its C-terminal flexible tail, which is known to mediate protein-protein interactions. In live-cell imaging studies, an A5-mCherry chromobody colocalizes with NEIL1-GFP and is recruited to sites of laser-induced DNA damage, suggesting its potential as a molecular tool for visualizing NEIL1 dynamics. These findings establish A5 as a valuable probe for studying NEIL1 function and opens new avenues for exploring its role in DNA repair.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"150 ","pages":"Article 103849"},"PeriodicalIF":3.0,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144169572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Overexpression of the WWE domain of RNF146 modulates poly-(ADP)-ribose dynamics at sites of DNA damage RNF146的WWE结构域的过表达可调节DNA损伤位点的多核苷酸动力学

IF 3 3区生物学

DNA Repair Pub Date : 2025-05-21 DOI: 10.1016/j.dnarep.2025.103845

Rasha Q. Al-Rahahleh , Wynand P. Roos , Kate M. Saville , Joel F. Andrews , Zhijin Wu , Christopher A. Koczor , Aishwarya Prakash , Robert W. Sobol

{"title":"Overexpression of the WWE domain of RNF146 modulates poly-(ADP)-ribose dynamics at sites of DNA damage","authors":"Rasha Q. Al-Rahahleh , Wynand P. Roos , Kate M. Saville , Joel F. Andrews , Zhijin Wu , Christopher A. Koczor , Aishwarya Prakash , Robert W. Sobol","doi":"10.1016/j.dnarep.2025.103845","DOIUrl":"10.1016/j.dnarep.2025.103845","url":null,"abstract":"<div><div>Protein poly-ADP-ribosylation (PARylation) is a post-translational modification formed by transferring successive units of ADP-ribose to target proteins to form poly-ADP-ribose (PAR) chains. PAR plays a critical role in the DNA damage response (DDR) by acting as a signaling platform to promote the recruitment of DNA repair factors to the sites of DNA damage that bind via their PAR-binding domains (PBDs). Several classes of PBD families have been identified, which recognize distinct parts of the PAR chain. Proteins encoding PBDs play an essential role in conveying the PAR-mediated signal through their interaction with PAR chains, which mediates many cellular functions, including the DDR. The WWE domain, encoded in 12 human proteins, identifies the iso-ADP-ribose moiety of the PAR chain. PARylation is a heterogeneous structure that is highly dynamic in cells. Capturing the dynamics of PARylation is essential to understanding its role in the DDR, which can be achieved by expanding the tool kit for PAR detection and tracking mediated by the unique binding capability of various sensors. We recently described the WWE domain of RNF146 as a robust genetically encoded probe, when fused to EGFP, for the detection of PAR in live cells. Expanding on this, we used structural prediction tools to evaluate all of the WWE domains encoded in human proteins, evaluating each as molecular PAR probes in live cells. We demonstrate unique PAR dynamics when tracked by WWE-encoded PAR binding domains, in addition to an engineered macrodomain, that can be exploited for modulation of the PAR-dependent DNA damage response.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"150 ","pages":"Article 103845"},"PeriodicalIF":3.0,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144106402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PARP1-PROTACs providing novel opportunities in precision oncology by targeting DNA damage response PARP1-PROTACs通过靶向DNA损伤反应为精确肿瘤学提供了新的机会

IF 3 3区生物学

DNA Repair Pub Date : 2025-05-21 DOI: 10.1016/j.dnarep.2025.103851

Md Sadique Hussain, Gaurav Gupta

引用次数: 0

BRCA1 and BRCA2 in DNA damage and replication stress response: Insights into their functions, mechanisms, and implications for cancer treatment BRCA1和BRCA2在DNA损伤和复制应激反应中的作用、机制及其对癌症治疗的影响

IF 3 3区生物学

DNA Repair Pub Date : 2025-05-13 DOI: 10.1016/j.dnarep.2025.103847

Ziqi Xu , Haihua Xie , Lizhi Song , Yuhua Huang , Jun Huang

{"title":"BRCA1 and BRCA2 in DNA damage and replication stress response: Insights into their functions, mechanisms, and implications for cancer treatment","authors":"Ziqi Xu , Haihua Xie , Lizhi Song , Yuhua Huang , Jun Huang","doi":"10.1016/j.dnarep.2025.103847","DOIUrl":"10.1016/j.dnarep.2025.103847","url":null,"abstract":"<div><div>Genomic stability is a cornerstone of cellular survival and proliferation. To counter the constant threat posed by endogenous and exogenous DNA-damaging agents, cells rely on a network of intricate mechanisms to safeguard DNA integrity and ensure accurate replication. Among these, the BRCA1 and BRCA2 tumor suppressor proteins play pivotal roles. While traditionally recognized for their involvement in homologous recombination repair and cell cycle checkpoints, emerging evidence highlights their essential functions in protecting stalled replication forks during replication stress. Mutations in BRCA1 or BRCA2 disrupt these critical functions, leading to compromised genome stability and an increased susceptibility to various cancers, particularly breast and ovarian cancers. This review provides a comprehensive analysis of the multifaceted roles of BRCA1 and BRCA2, focusing on their contributions to DNA damage responses and replication stress management. By elucidating the molecular pathways through which BRCA1 and BRCA2 operate, we aim to provide insights into their pivotal roles in maintaining genomic integrity and their implications for cancer treatment.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"150 ","pages":"Article 103847"},"PeriodicalIF":3.0,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143947293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Emerging connections: Poly(ADP-ribose), FET proteins and RNA in the regulation of DNA damage condensates 新出现的联系：聚（adp -核糖），FET蛋白和RNA在DNA损伤凝聚体的调节

IF 3 3区生物学

DNA Repair Pub Date : 2025-05-08 DOI: 10.1016/j.dnarep.2025.103846

Silvia Lombardi, Mara Zilocchi, Roland Nicsanu, Silvia Maria Luisa Barabino

{"title":"Emerging connections: Poly(ADP-ribose), FET proteins and RNA in the regulation of DNA damage condensates","authors":"Silvia Lombardi, Mara Zilocchi, Roland Nicsanu, Silvia Maria Luisa Barabino","doi":"10.1016/j.dnarep.2025.103846","DOIUrl":"10.1016/j.dnarep.2025.103846","url":null,"abstract":"<div><div>Our genome is exposed to thousands of DNA lesions every day, posing a significant threat to cellular viability. To deal with these lesions, cells have evolved sophisticated repair mechanisms collectively known as the DNA damage response. DNA double-strand breaks (DSBs) are very cytotoxic damages, and their repair requires the precise and coordinated recruitment of multiple repair factors to form nuclear <em>foci</em>. Recent research highlighted that these repair structures behave as biomolecular condensates, <em>i.e.</em> membraneless compartments with liquid-like properties. The formation of condensates is driven by weak, multivalent interactions among proteins and nucleic acids, and recent studies highlighted the roles of poly(ADP-ribose) (PAR) and RNA in regulating DSBs-related condensates. Additionally, the FET family of RNA-binding proteins (including FUS, EWS and TAF15), has emerged as a critical player in the DNA damage response, with recent evidence suggesting that FET proteins support the formation and dynamics of repair condensates. Notably, phase separation of FET proteins is implicated also in their pathological functions in cancer biology, highlighting the pervasive role of condensation. This review will provide an overview of biomolecular condensates at DSBs, focusing on the interplay among PAR and RNA in the spatiotemporal regulation of FET proteins at repair complexes. We will also discuss the role of FET condensates in cancer biology and how they are targeted for therapeutic purposes. The study of biomolecular condensates holds great promise for advancing our understanding of key cellular processes and developing novel therapeutic strategies, but requires careful consideration of potential challenges.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"150 ","pages":"Article 103846"},"PeriodicalIF":3.0,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144068527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Targeting base excision repair in precision oncology 精准肿瘤学中靶向碱基切除修复

IF 3 3区生物学

DNA Repair Pub Date : 2025-05-01 DOI: 10.1016/j.dnarep.2025.103844

Nicola P. Montaldo , Hilde Loge Nilsen , Diana L. Bordin

引用次数: 0

Joining of DNA breaks- interplay between DNA ligases and poly (ADP-ribose) polymerases DNA断裂的连接- DNA连接酶和多聚核糖聚合酶之间的相互作用

IF 3 3区生物学

DNA Repair Pub Date : 2025-05-01 DOI: 10.1016/j.dnarep.2025.103843

Nicolas Call, Alan E. Tomkinson

{"title":"Joining of DNA breaks- interplay between DNA ligases and poly (ADP-ribose) polymerases","authors":"Nicolas Call, Alan E. Tomkinson","doi":"10.1016/j.dnarep.2025.103843","DOIUrl":"10.1016/j.dnarep.2025.103843","url":null,"abstract":"<div><div>The joining of DNA single- and double-strand breaks (SSB and DSB) is essential for maintaining genome stability and integrity. While this is ultimately accomplished in human cells by the DNA ligases encoded by the <em>LIG1</em>, <em>LIG3</em> and <em>LIG4</em> genes, these enzymes are recruited to DNA breaks through specific interactions with proteins involved in break sensing and recognition and/or break processing. In this review, we focus on the interplay between the DNA break-activated poly (ADP-ribose) polymerases, PARP1 and PARP2, poly (ADP-ribose) (PAR) and the DNA ligases in DNA replication and repair. The most extensively studied example of this interplay is the recruitment of DNA ligase IIIα (LigIIIα) and other repair proteins to SSBs through an interaction between XRCC1, a scaffold protein and partner protein of nuclear LigIIIα, and PAR synthesized by PARP1 and to a lesser extent PARP2. Recently, these proteins have been implicated in a back-up pathway for joining Okazaki fragments that appears to have a critical function even in cells with no defect in the major LigI-dependent pathway. Finally, we discuss the effects of FDA-approved PARP1/2 inhibitors on DNA replication and repair in cancer and non-malignant cells and the potential utility of DNA ligase inhibitors as cancer therapeutics.</div></div>","PeriodicalId":300,"journal":{"name":"DNA Repair","volume":"149 ","pages":"Article 103843"},"PeriodicalIF":3.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143923468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DNA Repair最新文献