Nucleic Acids Research最新文献_第9页

Correction to 'ADAR3 modulates neuronal differentiation and regulates mRNA stability and translation'. 修正“ADAR3调节神经元分化并调节mRNA的稳定性和翻译”。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-07 DOI: 10.1093/nar/gkae1284

引用次数: 0

Point mutations in functionally diverse genes are associated with increased natural DNA transformation in multidrug resistant Streptococcus pneumoniae. 功能多样化基因的点突变与耐多药肺炎链球菌的天然 DNA 转化增加有关。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-07 DOI: 10.1093/nar/gkae1140

Flora Peillard-Fiorente, Nguyen Phuong Pham, Hélène Gingras, Chantal Godin, Jie Feng, Philippe Leprohon, Marc Ouellette

{"title":"Point mutations in functionally diverse genes are associated with increased natural DNA transformation in multidrug resistant Streptococcus pneumoniae.","authors":"Flora Peillard-Fiorente, Nguyen Phuong Pham, Hélène Gingras, Chantal Godin, Jie Feng, Philippe Leprohon, Marc Ouellette","doi":"10.1093/nar/gkae1140","DOIUrl":"10.1093/nar/gkae1140","url":null,"abstract":"DNA transformation is key for phenotypic diversity and adaptation of Streptococcus pneumoniae including in the emergence of multidrug resistance (MDR). Under laboratory conditions, DNA transformation is facilitated by the artificial triggering of competence by the competence stimulating peptide (CSP). In ongoing DNA transformation work, we observed that exogenous CSP was dispensable depending on the combination of strains and culture media. Here, we carried out a chemogenomic screen to select for S. pneumoniae mutants capable of natural transformation in medium that normally would not sustain natural transformation. Our chemogenomic screen relied on chemical mutagenesis followed by selection of mutants with increased DNA transformation capacities. Sequencing the genome of these mutants revealed an abundance and diversity of mutated genes proven experimentally to increase natural transformation. A genome wide association study between MDR and sensitive clinical isolates revealed gene mutations associated with MDR, many of which intersected with those pinpointed by our chemogenomic screens and that were proven to increase natural transformation. S. pneumoniae has adopted DNA transformation as its lifestyle and can select for mutations facilitating DNA transformation.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11724299/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824110","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

Correction to 'Enhancing disease risk gene discovery by integrating transcription factor-linked trans-variants into transcriptome-wide association analyses'. 更正“通过将转录因子相关的反式变异整合到转录组全关联分析中来增强疾病风险基因的发现”。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-07 DOI: 10.1093/nar/gkae1239

引用次数: 0

Single-molecule analysis reveals that IPMK enhances the DNA-binding activity of the transcription factor SRF 单分子分析表明IPMK可增强转录因子SRF的dna结合活性

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-01-07 DOI: 10.1093/nar/gkae1281

Hyoungjoon Ahn, Jeongmin Yu, Kwangmin Ryu, Jaeseung Ryu, Sera Kim, Jae Yeong Park, Ji Kwang Kim, Inhong Jung, Haejin An, Sehoon Hong, Eunha Kim, Kihyun Park, Myunghwan Ahn, Sunwoo Min, Inkyung Jung, Daeyoup Lee, Thomas Lee, Youngjoo Byun, Ji-Joon Song, Jaehoon Kim, Won-Ki Cho, Gwangrog Lee, Seyun Kim

{"title":"Single-molecule analysis reveals that IPMK enhances the DNA-binding activity of the transcription factor SRF","authors":"Hyoungjoon Ahn, Jeongmin Yu, Kwangmin Ryu, Jaeseung Ryu, Sera Kim, Jae Yeong Park, Ji Kwang Kim, Inhong Jung, Haejin An, Sehoon Hong, Eunha Kim, Kihyun Park, Myunghwan Ahn, Sunwoo Min, Inkyung Jung, Daeyoup Lee, Thomas Lee, Youngjoo Byun, Ji-Joon Song, Jaehoon Kim, Won-Ki Cho, Gwangrog Lee, Seyun Kim","doi":"10.1093/nar/gkae1281","DOIUrl":"https://doi.org/10.1093/nar/gkae1281","url":null,"abstract":"Serum response factor (SRF) is a master transcription factor that regulates immediate early genes and cytoskeletal remodeling genes. Despite its importance, the mechanisms through which SRF stably associates with its cognate promoter remain unknown. Our biochemical and protein-induced fluorescence enhancement analyses showed that the binding of SRF to serum response element was significantly increased by inositol polyphosphate multikinase (IPMK), an SRF cofactor. Moreover, real-time tracking of SRF loci in live cell nuclei demonstrated that the chromatin residence time of SRF was reduced by IPMK depletion in fibroblasts. Conversely, elevated IPMK levels extended the SRF–chromatin association. We identified that IPMK binds to the intrinsically disordered region of SRF, which is required for the IPMK-induced stable interaction of SRF with DNA. IPMK-mediated conformational changes in SRF were observed by single-molecule fluorescence resonance energy transfer assays. Therefore, our findings demonstrate that IPMK is a critical factor for promoting high-affinity SRF–chromatin association and provide insights into the mechanisms of SRF-dependent transcription control via chaperone-like activity.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"1 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142935934","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

Cell cycle progression of under-replicated cells. 欠复制细胞的细胞周期进程。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-07 DOI: 10.1093/nar/gkae1311

Min Huang, Chang Yang, Litong Nie, Huimin Zhang, Dandan Zhu, Chao Wang, Jeong-Min Park, Mrinal Srivastava, Elina Mosa, Siting Li, Mengfan Tang, Xu Feng, Sarah J Keast, Fabio Stossi, Junjie Chen

引用次数: 0

Correction to 'The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis'. 斑马鱼早期胚胎发育过程中细胞命运规范的染色质可及性动态 "的更正

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-07 DOI: 10.1093/nar/gkae1286

引用次数: 0

DIONYSUS: a database of protein-carbohydrate interfaces. DIONYSUS：蛋白质-碳水化合物界面数据库。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-06 DOI: 10.1093/nar/gkae890

Aria Gheeraert, Thomas Bailly, Yani Ren, Ali Hamraoui, Julie Te, Yann Vander Meersche, Gabriel Cretin, Ravy Leon Foun Lin, Jean-Christophe Gelly, Serge Pérez, Frédéric Guyon, Tatiana Galochkina

{"title":"DIONYSUS: a database of protein-carbohydrate interfaces.","authors":"Aria Gheeraert, Thomas Bailly, Yani Ren, Ali Hamraoui, Julie Te, Yann Vander Meersche, Gabriel Cretin, Ravy Leon Foun Lin, Jean-Christophe Gelly, Serge Pérez, Frédéric Guyon, Tatiana Galochkina","doi":"10.1093/nar/gkae890","DOIUrl":"10.1093/nar/gkae890","url":null,"abstract":"Protein-carbohydrate interactions govern a wide variety of biological processes and play an essential role in the development of different diseases. Here, we present DIONYSUS, the first database of protein-carbohydrate interfaces annotated according to structural, chemical and functional properties of both proteins and carbohydrates. We provide exhaustive information on the nature of interactions, binding site composition, biological function and specific additional information retrieved from existing databases. The user can easily search the database using protein sequence and structure information or by carbohydrate binding site properties. Moreover, for a given interaction site, the user can perform its comparison with a representative subset of non-covalent protein-carbohydrate interactions to retrieve information on its potential function or specificity. Therefore, DIONYSUS is a source of valuable information both for a deeper understanding of general protein-carbohydrate interaction patterns, for annotation of the previously unannotated proteins and for such applications as carbohydrate-based drug design. DIONYSUS is freely available at www.dsimb.inserm.fr/DIONYSUS/.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":"D387-D395"},"PeriodicalIF":16.6,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11701518/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142471255","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

CTR-DB 2.0: an updated cancer clinical transcriptome resource, expanding primary drug resistance and newly adding acquired resistance datasets and enhancing the discovery and validation of predictive biomarkers. CTR-DB 2.0：更新的癌症临床转录组资源，扩展了原发性耐药性数据集，并新增加了获得的耐药性数据集，加强了预测性生物标志物的发现和验证。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-06 DOI: 10.1093/nar/gkae993

Jianzhou Jiang, Yajie Ma, Lele Yang, Shurui Ma, Zixuan Yu, Xinyi Ren, Xiangya Kong, Xinlei Zhang, Dong Li, Zhongyang Liu

{"title":"CTR-DB 2.0: an updated cancer clinical transcriptome resource, expanding primary drug resistance and newly adding acquired resistance datasets and enhancing the discovery and validation of predictive biomarkers.","authors":"Jianzhou Jiang, Yajie Ma, Lele Yang, Shurui Ma, Zixuan Yu, Xinyi Ren, Xiangya Kong, Xinlei Zhang, Dong Li, Zhongyang Liu","doi":"10.1093/nar/gkae993","DOIUrl":"10.1093/nar/gkae993","url":null,"abstract":"Drug resistance is a principal limiting factor in cancer treatment. CTR-DB, the Cancer Treatment Response gene signature DataBase, is the first data resource for clinical transcriptomes with cancer treatment response, and meanwhile supports various data analysis functions, providing insights into the molecular determinants of drug resistance. Here we proposed an upgraded version, CTR-DB 2.0 (http://ctrdb.ncpsb.org.cn). Around 190 up-to-date source datasets with primary resistance information (129% increase compared to version 1.0) and 13 acquired-resistant datasets (a new dataset type), covering 10 856 patient samples (111% increase), 39 cancer types (39% increase) and 346 therapeutic regimens (26% increase), have been collected. In terms of function, for the single dataset analysis and multiple-dataset comparison modules, CTR-DB 2.0 added new gene set enrichment, tumor microenvironment (TME) and signature connectivity analysis functions to help elucidate drug resistance mechanisms and their homogeneity/heterogeneity and discover candidate combinational therapies. Furthermore, biomarker-related functions were greatly extended. CTR-DB 2.0 newly supported the validation of cell types in the TME as predictive biomarkers of treatment response, especially the validation of a combinational biomarker panel and even the direct discovery of the optimal biomarker panel using user-customized CTR-DB patient samples. In addition, the analysis of users' own datasets, application programming interface and data crowdfunding were also added.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":"D1335-D1347"},"PeriodicalIF":16.6,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11701710/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142569179","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

DNAproDB: an updated database for the automated and interactive analysis of protein-DNA complexes. DNAproDB：用于自动和交互式分析蛋白质-DNA 复合物的最新数据库。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-06 DOI: 10.1093/nar/gkae970

Raktim Mitra, Ari S Cohen, Jared M Sagendorf, Helen M Berman, Remo Rohs

引用次数: 0

MolBiC: the cell-based landscape illustrating molecular bioactivities. MolBiC：基于细胞的分子生物活性图谱。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-01-06 DOI: 10.1093/nar/gkae868

Yichao Ge, Mengjie Yang, Xinyuan Yu, Ying Zhou, Yintao Zhang, Minjie Mou, Zhen Chen, Xiuna Sun, Feng Ni, Tingting Fu, Shuiping Liu, Lianyi Han, Feng Zhu

引用次数: 0