Nucleic Acids Research最新文献_第4页

Extensive homologous recombination safeguards oocyte genome integrity in mammals 广泛的同源重组保护了哺乳动物卵母细胞基因组的完整性

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-01-11 DOI: 10.1093/nar/gkae1304

Huiwen Cao, Cheng Qiu, Anxuan Fang, Jianzhou Shang, Wei Xu, Lugeng He, Xing Duan, Qianting Zhang, Chao Yu

{"title":"Extensive homologous recombination safeguards oocyte genome integrity in mammals","authors":"Huiwen Cao, Cheng Qiu, Anxuan Fang, Jianzhou Shang, Wei Xu, Lugeng He, Xing Duan, Qianting Zhang, Chao Yu","doi":"10.1093/nar/gkae1304","DOIUrl":"https://doi.org/10.1093/nar/gkae1304","url":null,"abstract":"Meiosis in mammalian oocytes is interrupted by a prolonged arrest at the germinal vesicle stage, during which oocytes have to repair DNA lesions to ensure genome integrity or otherwise undergo apoptosis. The FIRRM/FLIP-FIGNL1 complex dissociates RAD51 from the joint DNA molecules in both homologous recombination (HR) and DNA replication. However, as a type of non-meiotic, non-replicative cells, whether this RAD51-dismantling mechanism regulates genome integrity in oocytes remains elusive. Here, we show that FIRRM/FLIP is required for disassembly of RAD51-filaments and maintenance of genome integrity in oocytes. Deletion of FIRRM in oocytes leads to formation of massive nuclear RAD51 foci in oocytes of primordial follicles and activated follicles in mice. These RAD51 foci colocalize with the sites of DNA damage repair, as indicated by RPA2 and EdU, suggesting substantial DNA damage and extensive HR in oocytes. Especially in fully-grown FIRRM-deleted oocytes, RAD51 forms a net-like structure. As a consequence, FIRRM-deleted females are infertile due to aberrant homologous chromosome segregation at metaphase I and primordial follicle insufficiency at young adulthood. Hence, our study demonstrates the physiological importance of HR in maintaining genome integrity in oocytes.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"15 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142961617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Negative DNA supercoiling enhances DARS2 binding of DNA-bending protein IHF in the activation of Fis-dependent ATP-DnaA production 负DNA超卷曲增强了DNA弯曲蛋白IHF的DARS2结合，激活了fish依赖性atp - DNA的产生

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-01-11 DOI: 10.1093/nar/gkae1291

Kazutoshi Kasho, Kenya Miyoshi, Mizuki Yoshida, Ryuji Sakai, Sho Nakagawa, Tsutomu Katayama

{"title":"Negative DNA supercoiling enhances DARS2 binding of DNA-bending protein IHF in the activation of Fis-dependent ATP-DnaA production","authors":"Kazutoshi Kasho, Kenya Miyoshi, Mizuki Yoshida, Ryuji Sakai, Sho Nakagawa, Tsutomu Katayama","doi":"10.1093/nar/gkae1291","DOIUrl":"https://doi.org/10.1093/nar/gkae1291","url":null,"abstract":"Oscillation of the active form of the initiator protein DnaA (ATP-DnaA) allows for the timely regulation for chromosome replication. After initiation, DnaA-bound ATP is hydrolyzed, producing inactive ADP-DnaA. For the next round of initiation, ADP-DnaA interacts with the chromosomal locus DARS2 bearing binding sites for DnaA, a DNA-bending protein IHF, and a transcription activator Fis. The IHF binding site is about equidistant between the DnaA and Fis binding sites within DARS2. The DARS2-IHF-Fis complex promotes ADP dissociation from DnaA and furnishes ATP-DnaA at the pre-initiation stage, which dissociates Fis in a negative-feedback manner. However, regulation for IHF binding as well as mechanistic roles of Fis and specific DNA structure at DARS2 remain largely unknown. We have discovered that negative DNA supercoiling of DARS2 is required for stimulating IHF binding and ADP dissociation from DnaA in vitro. Consistent with these, novobiocin, a DNA gyrase inhibitor, inhibits DARS2 function in vivo. Fis Gln68, an RNA polymerase-interaction site, is suggested to be required for interaction with DnaA and full DARS2 activation. Based on these and other results, we propose that DNA supercoiling activates DARS2 function by stimulating stable IHF binding and DNA loop formation, thereby directing specific Fis–DnaA interaction.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"90 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142961645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Evidence for intrinsic DNA dynamics and deformability in damage sensing by the Rad4/XPC nucleotide excision repair complex Rad4/XPC核苷酸切除修复复合体损伤感知中DNA内在动力学和可变形性的证据

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-01-11 DOI: 10.1093/nar/gkae1290

Saroj Baral, Sagnik Chakraborty, Peter J Steinbach, Debamita Paul, Jung-Hyun Min, Anjum Ansari

{"title":"Evidence for intrinsic DNA dynamics and deformability in damage sensing by the Rad4/XPC nucleotide excision repair complex","authors":"Saroj Baral, Sagnik Chakraborty, Peter J Steinbach, Debamita Paul, Jung-Hyun Min, Anjum Ansari","doi":"10.1093/nar/gkae1290","DOIUrl":"https://doi.org/10.1093/nar/gkae1290","url":null,"abstract":"Altered DNA dynamics at lesion sites are implicated in how DNA repair proteins sense damage within genomic DNA. Using laser temperature-jump (T-jump) spectroscopy combined with cytosine-analog Förster Resonance Energy Transfer (FRET) probes that sense local DNA conformations, we measured the intrinsic dynamics of DNA containing 3 base-pair mismatches recognized in vitro by Rad4 (yeast ortholog of XPC). Rad4/XPC recognizes diverse lesions from environmental mutagens and initiates nucleotide excision repair. T-jump measurements, together with a novel and rigorous comparison with equilibrium FRET, uncovered conformational dynamics spanning multiple timescales and revealed key differences between Rad4-specific and non-specific DNA. AT-rich non-specific sites (matched or mismatched) exhibited dynamics primarily within the T-jump observation window, albeit with some amplitude in ‘missing’ fast (&lt;20 μs) kinetics. These fast-kinetics amplitudes were dramatically larger for specific sites (CCC/CCC and TTT/TTT), which also exhibited ‘missing’ slow (&gt;50 ms) kinetics at elevated temperatures, unseen in non-specific sites. We posit that the rapid (μs–ms) intrinsic DNA fluctuations help stall a diffusing protein at AT-rich/damaged sites and that the &gt;50-ms kinetics in specific DNA reflect a propensity to adopt unwound/bent conformations resembling Rad4-bound DNA structures. These studies provide compelling evidence for sequence/structure-dependent intrinsic DNA dynamics and deformability that likely govern damage sensing by Rad4.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"26 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142961646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Synthetic rational design of live-attenuated Zika viruses based on a computational model 基于计算模型的寨卡病毒减毒活病毒综合合理设计

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-01-11 DOI: 10.1093/nar/gkae1313

Modi Roopin, Zohar Zafrir, Bunpote Siridechadilok, Amporn Suphatrakul, Justin Julander, Tamir Tuller

{"title":"Synthetic rational design of live-attenuated Zika viruses based on a computational model","authors":"Modi Roopin, Zohar Zafrir, Bunpote Siridechadilok, Amporn Suphatrakul, Justin Julander, Tamir Tuller","doi":"10.1093/nar/gkae1313","DOIUrl":"https://doi.org/10.1093/nar/gkae1313","url":null,"abstract":"Many viruses of the Flaviviridae family, including the Zika virus (ZIKV), are human pathogens of significant public health concerns. Despite extensive research, there are currently no approved vaccines available for ZIKV and specifically no live-attenuated Zika vaccine. In this current study, we suggest a novel computational algorithm for generating live-attenuated vaccines via the introduction of silent mutation into regions that undergo selection for strong or weak local RNA folding or into regions that exhibit medium levels of sequence conservation. By implementing our approach to the ZIKV genome, we demonstrated strong correlation between the degree of conserved RNA local energy disruption and replicative ability of the viruses in Vero cells. In vivo analysis in the AG129 mouse model demonstrated the ability of the attenuated ZIKV strains to stimulate protective immune response against the wild-type virus. In some cases, up to 80% of the AG129 mice survived both the vaccination and the challenge with the wild-type strains, while 0% of the nonvaccinated mice survived the challenge. Our study provides a blueprint for a computational design of live-attenuated vaccine strains that still preserve immunogenic epitopes of the original RNA viruses. We believe that the approach is generic and can be used successfully for additional viruses.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"40 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142961647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Enhanced detection and genotyping of disease-associated tandem repeats using HMMSTR and targeted long-read sequencing. 利用 HMMSTR 和靶向长读数测序增强疾病相关串联重复序列的检测和基因分型。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-11 DOI: 10.1093/nar/gkae1202

Kinsey Van Deynze, Camille Mumm, Connor J Maltby, Jessica A Switzenberg, Peter K Todd, Alan P Boyle

{"title":"Enhanced detection and genotyping of disease-associated tandem repeats using HMMSTR and targeted long-read sequencing.","authors":"Kinsey Van Deynze, Camille Mumm, Connor J Maltby, Jessica A Switzenberg, Peter K Todd, Alan P Boyle","doi":"10.1093/nar/gkae1202","DOIUrl":"10.1093/nar/gkae1202","url":null,"abstract":"Tandem repeat sequences comprise approximately 8% of the human genome and are linked to more than 50 neurodegenerative disorders. Accurate characterization of disease-associated repeat loci remains resource intensive and often lacks high resolution genotype calls. We introduce a multiplexed, targeted nanopore sequencing panel and HMMSTR, a sequence-based tandem repeat copy number caller which outperforms current signal- and sequence-based callers relative to two assemblies and we show it performs with high accuracy in heterozygous regions and at low read coverage. The flexible panel allows us to capture disease associated regions at an average coverage of >150x. Using these tools, we successfully characterize known or suspected repeat expansions in patient derived samples. In these samples, we also identify unexpected expanded alleles at tandem repeat loci not previously associated with the underlying diagnosis. This genotyping approach for tandem repeat expansions is scalable, simple, flexible and accurate, offering significant potential for diagnostic applications and investigation of expansion co-occurrence in neurodegenerative disorders.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142829327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Deciphering repair pathways of clustered DNA damage in human TK6 cells: insights from atomic force microscopy direct visualization 解读人类TK6细胞簇状DNA损伤的修复途径：原子力显微镜直接可视化的见解

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-01-11 DOI: 10.1093/nar/gkae1077

Toshiaki Nakano, Ken Akamatsu, Masaoki Kohzaki, Masataka Tsuda, Ryoichi Hirayama, Akira Sassa, Manabu Yasui, Mahmoud I Shoulkamy, Takeshi Hiromoto, Taro Tamada, Hiroshi Ide, Naoya Shikazono

{"title":"Deciphering repair pathways of clustered DNA damage in human TK6 cells: insights from atomic force microscopy direct visualization","authors":"Toshiaki Nakano, Ken Akamatsu, Masaoki Kohzaki, Masataka Tsuda, Ryoichi Hirayama, Akira Sassa, Manabu Yasui, Mahmoud I Shoulkamy, Takeshi Hiromoto, Taro Tamada, Hiroshi Ide, Naoya Shikazono","doi":"10.1093/nar/gkae1077","DOIUrl":"https://doi.org/10.1093/nar/gkae1077","url":null,"abstract":"Ionizing radiation induces various types of DNA damage, and the reparability and lethal effects of DNA damage differ depending on its spatial density. Elucidating the structure of radiation-induced clustered DNA damage and its repair processes will enhance our understanding of the lethal impact of ionizing radiation and advance progress toward precise therapeutics. Previously, we developed a method to directly visualize DNA damage using atomic force microscopy (AFM) and classified clustered DNA damage into simple base damage clusters (BDCs), complex BDCs and complex double-strand breaks (DSBs). This study investigated the repair of each type of damage in DNA-repair-deficient human TK6 cells and elucidated the association between each type of clustered DNA damage and the pathway responsible for its repair postirradiation with low linear energy transfer (LET) radiation (X-rays) and high-LET radiation (Fe-ion beams) in cells. We found that base excision repair and, surprisingly, nucleotide excision repair restored simple and complex BDCs. In addition, the number of complex DSBs in wild-type cells increases 1 h postirradiation, which was most likely caused by BDC cleavage initiated with DNA glycosylases. Furthermore, complex DSBs, which are likely associated with lethality, are repaired by homologous recombination with little contribution from nonhomologous-end joining.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"87 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142962801","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation. CRISPR-Cas12a在目标审讯期间使DNA弯曲以破坏碱基对的稳定。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-11 DOI: 10.1093/nar/gkae1192

Katarzyna M Soczek, Joshua C Cofsky, Owen T Tuck, Honglue Shi, Jennifer A Doudna

{"title":"CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation.","authors":"Katarzyna M Soczek, Joshua C Cofsky, Owen T Tuck, Honglue Shi, Jennifer A Doudna","doi":"10.1093/nar/gkae1192","DOIUrl":"10.1093/nar/gkae1192","url":null,"abstract":"RNA-guided endonucleases are involved in processes ranging from adaptive immunity to site-specific transposition and have revolutionized genome editing. CRISPR-Cas9, -Cas12 and related proteins use guide RNAs to recognize ∼20-nucleotide target sites within genomic DNA by mechanisms that are not yet fully understood. We used structural and biochemical methods to assess early steps in DNA recognition by Cas12a protein-guide RNA complexes. We show here that Cas12a initiates DNA target recognition by bending DNA to induce transient nucleotide flipping that exposes nucleobases for DNA-RNA hybridization. Cryo-EM structural analysis of a trapped Cas12a-RNA-DNA surveillance complex and fluorescence-based conformational probing show that Cas12a-induced DNA helix destabilization enables target discovery and engagement. This mechanism of initial DNA interrogation resembles that of CRISPR-Cas9 despite distinct evolutionary origins and different RNA-DNA hybridization directionality of these enzyme families. Our findings support a model in which RNA-mediated DNA interference begins with local helix distortion by transient CRISPR-Cas protein binding.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142854788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Protein-free catalysis of DNA hydrolysis and self-integration by a ribozyme. 核酶对DNA水解和自整合的无蛋白催化作用。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-11 DOI: 10.1093/nar/gkae1224

Deni Szokoli, Hannes Mutschler

{"title":"Protein-free catalysis of DNA hydrolysis and self-integration by a ribozyme.","authors":"Deni Szokoli, Hannes Mutschler","doi":"10.1093/nar/gkae1224","DOIUrl":"10.1093/nar/gkae1224","url":null,"abstract":"Group II introns are ancient self-splicing ribozymes and retrotransposons. Though long speculated to have originated before translation, their dependence on intron-encoded proteins for splicing and mobility has cast doubt on this hypothesis. While some group II introns are known to retain part of their catalytic repertoire in the absence of protein cofactors, protein-free complete reverse splicing of a group II intron into a DNA target has never been demonstrated. Here, we demonstrate the complete independence of a group II intron from protein cofactors in all intron-catalyzed reactions. The ribozyme is capable of fully reverse splicing into single-stranded DNA targets in vitro, readily hydrolyzes DNA substrates and is even able to unwind and react with stably duplexed DNA. Our findings make a protein-free origin for group II introns plausible by expanding their known catalytic capabilities beyond what would be needed to survive the transition from RNA to DNA genomes. Furthermore, the intron's capacity to react with both single and double-stranded DNA in conjunction with its expanded sequence recognition may represent a promising starting point for the development of protein-free genomic editing tools.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142854830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Alkylated DNA repair by a novel HhH-GPD family protein from Crenarchaea.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-11 DOI: 10.1093/nar/gkaf012

Likui Zhang, Tian Gao, Zheng Li, Cai Chen, Donghao Jiang, Youcheng Yin, Yaqi Zheng, Peng Cao, Yong Gong, Zhihui Yang

{"title":"Alkylated DNA repair by a novel HhH-GPD family protein from Crenarchaea.","authors":"Likui Zhang, Tian Gao, Zheng Li, Cai Chen, Donghao Jiang, Youcheng Yin, Yaqi Zheng, Peng Cao, Yong Gong, Zhihui Yang","doi":"10.1093/nar/gkaf012","DOIUrl":"https://doi.org/10.1093/nar/gkaf012","url":null,"abstract":"HhH-GPD (helix-hairpin-helix-glycine/proline/aspartate) family proteins are involved in DNA damage repair. Currently, mechanism of alkylated DNA repair in Crenarchaea has not been fully clarified. The hyperthermophilic model crenarchaeon Saccharolobus islandicus REY15A possesses a novel HhH-GPD family protein (Sis-HhH-GPD), where its Ser152 corresponds to a conserved catalytic Asp in other HhH-GPD homologs. Herein, we report that Sis-HhH-GPD is a novel bi-functional glycosylase, capable of removing both 1-methyladenine (1-meA) from DNA and alkylated bases from DNA created by methyl methanesulfonate (MMS). Mutational analyses show that E134 is essential for catalysis, whereas S152 is not essential. Sis-HhH-GPD might utilize aromatic rings of Y154 and W57 to stack against 1-meA base for flipping-out and then be removed by E134. Additionally, R157, R161 and R200 participate in catalysis. Among four cysteine residues that potentially coordinate with the Fe-S cluster loop, C203, C210 and C219 are involved in catalysis. Importantly, Sis-HhH-GPD is responsible for repair of alkylated DNA created by MMS in vivo. Interestingly, genetic complementary data have confirmed physiological function of Sis-HhH-GPD in alkylated DNA repair and clarified functional roles of its four cysteine residues in vivo. Overall, we provide first evidence that HhH-GPD family protein from Crenarchaea functions in alkylated DNA repair.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 2","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143024038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

TDP1 splice-site mutation causes HAP1 cell hypersensitivity to topoisomerase I inhibition. TDP1剪接位点突变引起HAP1细胞对拓扑异构酶I抑制的超敏反应。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-11 DOI: 10.1093/nar/gkae1163

Chen Gang Goh, Aldo S Bader, Tuan-Anh Tran, Rimma Belotserkovskaya, Giuseppina D'Alessandro, Stephen P Jackson

{"title":"TDP1 splice-site mutation causes HAP1 cell hypersensitivity to topoisomerase I inhibition.","authors":"Chen Gang Goh, Aldo S Bader, Tuan-Anh Tran, Rimma Belotserkovskaya, Giuseppina D'Alessandro, Stephen P Jackson","doi":"10.1093/nar/gkae1163","DOIUrl":"10.1093/nar/gkae1163","url":null,"abstract":"HAP1 is a near-haploid human cell line commonly used for mutagenesis and genome editing studies due to its hemizygous nature. We noticed an unusual hypersensitivity of HAP1 to camptothecin, an antineoplastic drug that stabilizes topoisomerase I cleavage complexes (TOP1ccs). We have attributed this hypersensitivity to a deficiency of TDP1, a key phosphodiesterase involved in resolving abortive TOP1ccs. Through whole-exome sequencing and subsequent restoration of TDP1 protein via CRISPR-Cas9 endogenous genome editing, we demonstrate that TDP1 deficiency and camptothecin hypersensitivity in HAP1 cells are a result of a splice-site mutation (TDP1 c.660-1G > A) that causes exon skipping and TDP1 loss of function. The lack of TDP1 in HAP1 cells should be considered when studying topoisomerase-associated DNA lesions and when generalizing mechanisms of DNA damage repair using HAP1 cells. Finally, we also report the generation of HAP1 STAR clones with restored TDP1 expression and function, which may be useful in further studies to probe cellular phenotypes relating to TOP1cc repair.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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