Nucleic Acids Research最新文献_第7页

Correction to 'CARM1/PRMT4 facilitates XPF-ERCC1 heterodimer assembly and maintains nucleotide excision repair activity'. 修正为“CARM1/PRMT4促进XPF-ERCC1异源二聚体组装并维持核苷酸切除修复活性”。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-05-22 DOI: 10.1093/nar/gkaf490

引用次数: 0

Quantitative spatial analysis of bacterial transcriptome and chromosome structural data with GRATIOSA: application to twin-supercoiled domain distribution. 利用GRATIOSA对细菌转录组和染色体结构数据进行定量空间分析：应用于双超螺旋结构域分布。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-05-22 DOI: 10.1093/nar/gkaf452

Maïwenn Pineau, Raphaël Forquet, Sylvie Reverchon, William Nasser, Florence Hommais, Sam Meyer

{"title":"Quantitative spatial analysis of bacterial transcriptome and chromosome structural data with GRATIOSA: application to twin-supercoiled domain distribution.","authors":"Maïwenn Pineau, Raphaël Forquet, Sylvie Reverchon, William Nasser, Florence Hommais, Sam Meyer","doi":"10.1093/nar/gkaf452","DOIUrl":"10.1093/nar/gkaf452","url":null,"abstract":"While classical models of transcriptional regulation focus on transcription factors binding at promoters, gene expression is also influenced by chromosome organization. Understanding this spatial regulation strongly benefits from integrated and quantitative spatial analyses of genome-scale data such as RNA-Seq and ChIP-Seq. We introduce Genome Regulation Analysis Tool Incorporating Organization and Spatial Architecture (GRATIOSA), a Python package making such combined analyses more systematic and reproducible. While current software focuses on initial analysis steps (read mapping and counting), GRATIOSA proposes an integrated framework for subsequent analyses, providing a broad range of spatially resolved quantitative data analyses, comparisons, and representations. Several tutorials illustrate applications across diverse species for typical tasks involving RNA-Seq, ChIP-Seq, and processed Hi-C data. We also use the software to quantitatively assess the validity and extension of the twin-supercoiled domain model in Escherichia coli genome-wide transcription, using recent topoisomerase ChIP-Seq data. We show that topoisomerases are locally recruited specifically by the 40% most highly expressed transcription units, with magnitudes correlating with expression levels. The recruitment of topoisomerase I extends to around 10 kb upstream, whereas DNA gyrase is recruited at least 30 kb downstream of transcription units, with subtle requirements for each enzyme depending on the orientation and expression level.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 10","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12125540/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144192087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

m6A modification is incorporated into bacterial mRNA without specific functional benefit. m6A修饰被合并到细菌mRNA中，没有特定的功能益处。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-05-22 DOI: 10.1093/nar/gkaf425

Klara Szydlo,Leonardo Santos,Thomas W Christian,Sunita Maharjan,Amir Dorsey,Isao Masuda,Jingxuan Jia,Yuan Wu,Weixin Tang,Ya-Ming Hou,Zoya Ignatova

{"title":"m6A modification is incorporated into bacterial mRNA without specific functional benefit.","authors":"Klara Szydlo,Leonardo Santos,Thomas W Christian,Sunita Maharjan,Amir Dorsey,Isao Masuda,Jingxuan Jia,Yuan Wu,Weixin Tang,Ya-Ming Hou,Zoya Ignatova","doi":"10.1093/nar/gkaf425","DOIUrl":"https://doi.org/10.1093/nar/gkaf425","url":null,"abstract":"N 6-Methyladenosine (m6A), the most abundant modification in eukaryotic messenger RNAs (mRNAs), has also been found at a low level in bacterial mRNAs. However, enzyme(s) that introduce m6A modification on mRNAs in bacteria remain elusive. In this work, we combine deep-sequencing approaches that identify m6A sites with in vitro biochemical studies to identify putative m6A methyltransferases that would modify Escherichia coli mRNAs. We tested four uncharacterized candidates predicted to encode proteins with putative methyltransferase domains, whose deletion decreased the m6A level. However, in vitro analysis with the purified putative methyltransferases revealed that none of them installs m6A on mRNA. Exposure to heat and oxidative stress also changed the m6A level; however, we found no clear correlation between the m6A change and the specific stress. Considering two deep-sequencing approaches with different resolution, we found that m6A methylation on bacterial mRNAs is very low and appears randomly introduced. These results suggest that, in contrast to eukaryotes, the m6A modification in bacterial mRNA lacks a direct enzymatic recognition mechanism and has no clear biological function.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"136 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144114271","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

3D genome organization shapes DNA damage susceptibility to platinum-based drugs. 三维基因组组织塑造DNA损伤对铂类药物的易感性。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-05-22 DOI: 10.1093/nar/gkaf315

Ye Wang, Asli Yildirim, Lorenzo Boninsegna, Valentina Christian, Sung-Hae L Kang, Xianghong Jasmine Zhou, Frank Alber

{"title":"3D genome organization shapes DNA damage susceptibility to platinum-based drugs.","authors":"Ye Wang, Asli Yildirim, Lorenzo Boninsegna, Valentina Christian, Sung-Hae L Kang, Xianghong Jasmine Zhou, Frank Alber","doi":"10.1093/nar/gkaf315","DOIUrl":"10.1093/nar/gkaf315","url":null,"abstract":"Platinum (Pt) drugs are widely utilized in cancer chemotherapy. Although cytotoxic and resistance mechanisms of Pt drugs have been thoroughly explored, it remains elusive what factors affect the receptiveness of DNA to drug-induced damage in nuclei. Here, we demonstrate that nuclear locations of chromatin play a key role in Pt drug-induced DNA damage susceptibility in vivo. By integrating data from damage-seq experiments with 3D genome structure information, we show that nuclear locations of chromatin relative to specific nuclear bodies and compartments explain patterns of cisplatin DNA damage susceptibility. This aligns with observations of cisplatin enrichment in biomolecular condensates at certain nuclear bodies. Finally, 3D structure mapping of DNA damage reveals characteristic differences between nuclear distributions of oxaliplatin-induced DNA damage in drug resistant versus sensitive cells. DNA damage increases in gene-poor chromatin at the nuclear periphery, while it decreases in gene-rich regions located at nuclear speckles. This suggests a strategic redistribution of Pt drug-induced damage in nuclei during chemoresistance development.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 10","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12117463/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144160620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Methyl-CODEC enables simultaneous methylation and duplex sequencing. 甲基- codec能够同时甲基化和双工测序。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-05-22 DOI: 10.1093/nar/gkaf482

Ruolin Liu, Farzaneh Darbeheshti, Laurel Walsh, Rachel Li, Jin H Bae, Hayet Radia Zeggar, Azeet Narayan, Kan Xiong, G Mike Makrigiorgos, Viktor A Adalsteinsson

{"title":"Methyl-CODEC enables simultaneous methylation and duplex sequencing.","authors":"Ruolin Liu, Farzaneh Darbeheshti, Laurel Walsh, Rachel Li, Jin H Bae, Hayet Radia Zeggar, Azeet Narayan, Kan Xiong, G Mike Makrigiorgos, Viktor A Adalsteinsson","doi":"10.1093/nar/gkaf482","DOIUrl":"10.1093/nar/gkaf482","url":null,"abstract":"DNA mutations and methylation often contribute to disease development in a synergistic manner. While duplex sequencing is the most accurate method for detecting DNA mutations, it typically lacks the ability to simultaneously assess methylation or requires many reads. Here, we developed Methyl-CODEC to enable simultaneous methylation sequencing and duplex sequencing using single read pairs. To achieve this, Methyl-CODEC links an enzymatically deaminated sense strand to the reverse complement of the antisense strand, which is protected from conversion by using conversion-resistant dCTPs in the strand linking step. Methyl-CODEC shows high concordance with standard enzymatic or bisulfite-based whole genome methylation sequencing, while also uniquely preserving the original DNA sequence. We show that hydroxy-methyl-dCTP is superior in this regard relative to other conversion-resistant dCTPs. Methyl-CODEC improves genetic sequencing accuracy, enables better read alignment for next-generation sequencing, and distinguishes C > T mutations from unmethylated Cs. It also identifies rare mutations including those producing methylated Cs, which are enriched in CpG contexts. Methyl-CODEC opens new horizons for enhanced detection of biomarkers in cancer and molecular medicine.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 10","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135180/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

GEPIA3: Enhanced drug sensitivity and interaction network analysis for cancer research. GEPIA3：用于癌症研究的增强药物敏感性和相互作用网络分析。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-05-21 DOI: 10.1093/nar/gkaf423

Yu-Jian Kang,Lingjie Pan,Yiyu Liu,Zhengqin Rong,Jiaxi Liu,Fenglin Liu

引用次数: 0

Quantum-inspired logic for advanced Transcriptional Programming 高级转录编程的量子启发逻辑

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-05-21 DOI: 10.1093/nar/gkaf440

Prasaad T Milner, Dowan Kim, Corey J Wilson

{"title":"Quantum-inspired logic for advanced Transcriptional Programming","authors":"Prasaad T Milner, Dowan Kim, Corey J Wilson","doi":"10.1093/nar/gkaf440","DOIUrl":"https://doi.org/10.1093/nar/gkaf440","url":null,"abstract":"The tenets of intelligent biological systems are (i) scalable decision-making, (ii) inheritable memory, and (iii) communication. This study aims to increase the complexity of decision-making operations beyond standard Boolean logic, while minimizing the metabolic burden imposed on the chassis cell. To this end, we present a new platform technology for constructing genetic circuits with multiple OUTPUT gene control using fewer INPUTs relative to conventional genetic circuits. Inspired by principles from quantum computing, we engineered synthetic bidirectional promoters, regulated by synthetic transcription factors, to construct 1-INPUT, 2-OUTPUT logical operations—i.e. biological QUBIT and PAULI-X logic gates—designed as compressed genetic circuits. We then layered said gates to engineer additional quantum-inspired logical operations of increasing complexity—e.g. FEYNMAN and TOFFOLI gates. In addition, we engineered a 2-INPUT, 4-OUTPUT quantum operation to showcase the capacity to utilize the entire permutation INPUT space. Finally, we developed a recombinase-based memory operation to remap the truth table between two disparate logic gates—i.e. converting a QUBIT operation to an antithetical PAULI-X operation in situ. This study introduces a novel and versatile synthetic biology toolkit, which expands the biocomputing capacity of Transcriptional Programming via the development of compressed and scalable multi-INPUT/OUTPUT logical operations.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"47 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144104610","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

SHARK: web server for alignment-free homology assessment for intrinsically disordered and unalignable protein regions. SHARK：用于对内在无序和不可对齐的蛋白质区域进行无比对同源性评估的web服务器。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-05-21 DOI: 10.1093/nar/gkaf408

Chi Fung Willis Chow,Maxim Scheremetjew,HongKee Moon,Soumyadeep Ghosh,Anna Hadarovich,Lena Hersemann,Agnes Toth-Petroczy

{"title":"SHARK: web server for alignment-free homology assessment for intrinsically disordered and unalignable protein regions.","authors":"Chi Fung Willis Chow,Maxim Scheremetjew,HongKee Moon,Soumyadeep Ghosh,Anna Hadarovich,Lena Hersemann,Agnes Toth-Petroczy","doi":"10.1093/nar/gkaf408","DOIUrl":"https://doi.org/10.1093/nar/gkaf408","url":null,"abstract":"Whereas alignment has been fundamental to sequence-based assessments of protein homology, it is ineffective for intrinsically disordered regions (IDRs) due to their lowered sequence conservation and unique sequence properties. Here, we present a web server implementation of SHARK (bio-shark.org), an alignment-free algorithm for homology classification that compares the overall amino acid composition and short regions (k-mers) shared between sequences (SHARK-scores). The output of such k-mer-based comparisons is used by SHARK-dive, a machine learning classifier to detect homology between unalignable, disordered sequences. SHARK-web provides sequence-versus-database assessment of protein sequence homology akin to conventional tools such as BLAST and HMMER. Additionally, we provide precomputed sets of IDR sequences from 16 model organism proteomes facilitating searches against species-specific IDR-omes. SHARK-dive offers superior overall homology detection performance to BLAST and HMMER, driven by a large increase in sensitivity to low sequence identity homologs, and can be used to facilitate the study of sequence-function relationships in disordered, difficult-to-align regions.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"18 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144103598","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

RegRNA 3.0: expanding regulatory RNA analysis with new features for motif, interaction, and annotation. RegRNA 3.0：扩展调控RNA分析与motif，相互作用和注释的新功能。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-05-21 DOI: 10.1093/nar/gkaf405

Yixian Huang,Zhiyong Zhang,Zhengkai Zou,Lingquan Zhang,Yigang Chen,Jingting Wan,Zihao Zhu,Sicong Yu,Huali Zuo,Yang-Chi-Dung Lin,Hsi-Yuan Huang,Hsien-Da Huang

{"title":"RegRNA 3.0: expanding regulatory RNA analysis with new features for motif, interaction, and annotation.","authors":"Yixian Huang,Zhiyong Zhang,Zhengkai Zou,Lingquan Zhang,Yigang Chen,Jingting Wan,Zihao Zhu,Sicong Yu,Huali Zuo,Yang-Chi-Dung Lin,Hsi-Yuan Huang,Hsien-Da Huang","doi":"10.1093/nar/gkaf405","DOIUrl":"https://doi.org/10.1093/nar/gkaf405","url":null,"abstract":"Functional RNA molecules are crucial for biological processes from gene regulation to protein synthesis, and analyzing functional motifs and elements is essential for understanding RNA regulation. Building on RegRNA 1.0 and 2.0, we present RegRNA 3.0, a sophisticated meta-workflow that integrates 26 computational tools and 28 databases for annotation, enabling one-step and customizable RNA motif predictions. RegRNA streamlines multi-step analysis and enhances result interpretation with interactive visualizations and comprehensive reporting tools. When provided with an RNA sequence, RegRNA 3.0 generates predictions for RNA functional motifs, RNA interaction motifs, and comprehensive RNA annotations. Specifically, RNA functional motifs include core promoter elements, RNA decay, G-quadruplex, and 14 previous types. RNA interaction motifs include newly added RNA-ligand interactions and RNA-binding protein predictions, along with three previous types. RNA annotation includes RNA family classification, blood exosomes RNA, subcellular localizations, A-to-I editing events, modifications, and 3D structures, along with four previously supported features. RegRNA 3.0 accelerates gene regulation and RNA biology discoveries by offering a user-friendly platform for identifying and analyzing RNA motifs and interactions. The web interface has been improved for intuitive visualizations of predicted motifs and structures, with flexible download options in multiple formats. It is available at http://awi.cuhk.edu.cn/∼RegRNA/.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"131 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144103541","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

hAb-Convergent: an antibody rearrangement analysis system for therapeutic antibody engineering based on convergent evolution. hAb-Convergent：基于收敛进化的治疗性抗体工程抗体重排分析系统。

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-05-21 DOI: 10.1093/nar/gkaf407

Jinfeng Wang,Xiaomeng Ge,Qinglan Sun,Minlong Chen,Shijie Qin,Dongmei Liu,Tao Deng,Juncai Ma,Songnian Hu,Ronghua Jin,Zhou Tong,Linhuan Wu

{"title":"hAb-Convergent: an antibody rearrangement analysis system for therapeutic antibody engineering based on convergent evolution.","authors":"Jinfeng Wang,Xiaomeng Ge,Qinglan Sun,Minlong Chen,Shijie Qin,Dongmei Liu,Tao Deng,Juncai Ma,Songnian Hu,Ronghua Jin,Zhou Tong,Linhuan Wu","doi":"10.1093/nar/gkaf407","DOIUrl":"https://doi.org/10.1093/nar/gkaf407","url":null,"abstract":"In therapeutic antibody engineering, utilizing naturally occurring mutations in the human body as a reference for modification is an emerging trend. The theory of convergent evolution presents a viable solution. Nevertheless, the nonuniformity of the antibody rearrangement analysis system and the difficulty in identifying the heavy-chain D-region are significant challenges to research and application. To address these limitations, we developed hAb (human antibody)-Convergent, a novel tool designed to assist users in quickly identifying candidate mutation hotspots of input antibody sequences in real human immune responses for subsequent antibody engineering. It uses antibody rearrangement features-based (V, D, J genes and CDR-H3 length) rather than traditional sequence-based strategies while ensuring the security of the original sequence. Combining more inclusive D-region identification and analysis methods, it can recognize and analyze the convergence of antibodies across various individuals. Additionally, given the limitations of obtaining antibody nucleotide sequences from academic literature, it provides an optimized approach for direct analysis and rapid comparison using amino acid sequences. hAb-Convergent bridges gaps in antibody engineering by linking natural evolution patterns to in vitro design, with implications for universal vaccine development. The tool can be freely accessed at https://nmdc.cn/zoe/.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"4 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144103540","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