Nucleic Acids Research最新文献

Profiling of i-motif-binding proteins reveals functional roles of nucleolin in regulation of high-order DNA structures. i-motif结合蛋白的剖析揭示了核仁蛋白在调控高阶DNA结构中的功能作用。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2024-11-19 DOI: 10.1093/nar/gkae1001

Yuki Ban, Yuka Ando, Yuma Terai, Risa Matsumura, Keita Nakane, Shigenori Iwai, Shinichi Sato, Junpei Yamamoto

{"title":"Profiling of i-motif-binding proteins reveals functional roles of nucleolin in regulation of high-order DNA structures.","authors":"Yuki Ban, Yuka Ando, Yuma Terai, Risa Matsumura, Keita Nakane, Shigenori Iwai, Shinichi Sato, Junpei Yamamoto","doi":"10.1093/nar/gkae1001","DOIUrl":"https://doi.org/10.1093/nar/gkae1001","url":null,"abstract":"Non-canonical DNA structures, such as the G-quadruplex (G4) and i-motif (iM), are formed at guanine- and cytosine-rich sequences, respectively, in living cells and involved in regulating various biological processes during the cell cycle. Therefore, the formation and resolution of these non-canonical structures must be dynamically regulated by physiological conditions or factors that can bind G4 and iM structures. Although many G4 binding proteins responsible for tuning the G4 structure have been discovered, the structural regulation of iM by iM-binding proteins remains enigmatic. In this study, we developed a protein-labeling DNA probe bearing an alkyne moiety through a reactive linker, for proximity-labeling of nucleic acid-binding proteins, and searched for new iM-binding proteins. Alkyne-modified proteins in the nuclear extract of HeLa cells were labeled with biotin via a click reaction and then captured with streptavidin-coated magnetic beads. This fingerprint-targeting enrichment, followed by proteome analyses, identified new candidate proteins that potentially bind to the iM structure, in addition to the reported iM-binding proteins. Among the newly identified candidates, we characterized a nucleolar protein, nucleolin, that binds to the iM structure and relaxes it, while nucleolin stabilizes the G4 structure.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668419","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

RADIP technology comprehensively identifies H3K27me3-associated RNA-chromatin interactions. RADIP 技术可全面识别与 H3K27me3 相关的 RNA 染色质相互作用。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2024-11-18 DOI: 10.1093/nar/gkae1054

Xufeng Shu, Masaki Kato, Satoshi Takizawa, Yutaka Suzuki, Piero Carninci

{"title":"RADIP technology comprehensively identifies H3K27me3-associated RNA-chromatin interactions.","authors":"Xufeng Shu, Masaki Kato, Satoshi Takizawa, Yutaka Suzuki, Piero Carninci","doi":"10.1093/nar/gkae1054","DOIUrl":"https://doi.org/10.1093/nar/gkae1054","url":null,"abstract":"Many RNAs associate with chromatin, either directly or indirectly. Several technologies for mapping regions where RNAs interact across the genome have been developed to investigate the function of these RNAs. Obtaining information on the proteins involved in these RNA-chromatin interactions is critical for further analysis. Here, we developed RADIP [RNA and DNA interacting complexes ligated and sequenced (RADICL-seq) with immunoprecipitation], a novel technology that combines RADICL-seq technology with chromatin immunoprecipitation to characterize RNA-chromatin interactions mediated by individual proteins. Building upon the foundational principles of RADICL-seq, RADIP extends its advantages by increasing genomic coverage and unique mapping rate efficiency compared to existing methods. To demonstrate its effectiveness, we applied an anti-H3K27me3 antibody to the RADIP technology and generated libraries from mouse embryonic stem cells (mESCs). We identified a multitude of RNAs, including RNAs from protein-coding genes and non-coding RNAs, that are associated with chromatin via H3K27me3 and that likely facilitate the spread of Polycomb repressive complexes over broad regions of the mammalian genome, thereby affecting gene expression, chromatin structures and pluripotency of mESCs. Our study demonstrates the applicability of RADIP to investigations of the functions of chromatin-associated RNAs.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668531","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

A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins. 深度突变扫描平台，用于描述抗 CRISPR 蛋白的适应性景观。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2024-11-18 DOI: 10.1093/nar/gkae1052

Tobias Stadelmann, Daniel Heid, Michael Jendrusch, Jan Mathony, Sabine Aschenbrenner, Stéphane Rosset, Bruno E Correia, Dominik Niopek

{"title":"A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins.","authors":"Tobias Stadelmann, Daniel Heid, Michael Jendrusch, Jan Mathony, Sabine Aschenbrenner, Stéphane Rosset, Bruno E Correia, Dominik Niopek","doi":"10.1093/nar/gkae1052","DOIUrl":"https://doi.org/10.1093/nar/gkae1052","url":null,"abstract":"Deep mutational scanning is a powerful method for exploring the mutational fitness landscape of proteins. Its adaptation to anti-CRISPR proteins, which are natural CRISPR-Cas inhibitors and key players in the co-evolution of microbes and phages, facilitates their characterization and optimization. Here, we developed a robust anti-CRISPR deep mutational scanning pipeline in Escherichia coli that combines synthetic gene circuits based on CRISPR interference with flow cytometry coupled sequencing and mathematical modeling. Using this pipeline, we characterized comprehensive single point mutation libraries for AcrIIA4 and AcrIIA5, two potent inhibitors of CRISPR-Cas9. The resulting mutational fitness landscapes revealed considerable mutational tolerance for both Acrs, suggesting an intrinsic redundancy with respect to Cas9 inhibitory features, and - for AcrIIA5 - indicated mutations that boost Cas9 inhibition. Subsequent in vitro characterization suggested that the observed differences in inhibitory potency between mutant inhibitors were mostly due to changes in binding affinity rather than protein expression levels. Finally, to demonstrate that our pipeline can inform Acrs-based genome editing applications, we employed a selected subset of mutant inhibitors to increase CRISPR-Cas9 target specificity by modulating Cas9 activity. Taken together, our work establishes deep mutational scanning as a powerful method for anti-CRISPR protein characterization and optimization.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668354","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

NASA open science data repository: open science for life in space. 美国国家航空航天局（NASA）开放科学数据储存库：太空生命开放科学。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2024-11-18 DOI: 10.1093/nar/gkae1116

Samrawit G Gebre, Ryan T Scott, Amanda M Saravia-Butler, Danielle K Lopez, Lauren M Sanders, Sylvain V Costes

{"title":"NASA open science data repository: open science for life in space.","authors":"Samrawit G Gebre, Ryan T Scott, Amanda M Saravia-Butler, Danielle K Lopez, Lauren M Sanders, Sylvain V Costes","doi":"10.1093/nar/gkae1116","DOIUrl":"https://doi.org/10.1093/nar/gkae1116","url":null,"abstract":"Space biology and health data are critical for the success of deep space missions and sustainable human presence off-world. At the core of effectively managing biomedical risks is the commitment to open science principles, which ensure that data are findable, accessible, interoperable, reusable, reproducible and maximally open. The 2021 integration of the Ames Life Sciences Data Archive with GeneLab to establish the NASA Open Science Data Repository significantly enhanced access to a wide range of life sciences, biomedical-clinical and mission telemetry data alongside existing 'omics data from GeneLab. This paper describes the new database, its architecture and new data streams supporting diverse data types and enhancing data submission, retrieval and analysis. Features include the biological data management environment for improved data submission, a new user interface, controlled data access, an enhanced API and comprehensive public visualization tools for environmental telemetry, radiation dosimetry data and 'omics analyses. By fostering global collaboration through its analysis working groups and training programs, the open science data repository promotes widespread engagement in space biology, ensuring transparency and inclusivity in research. It supports the global scientific community in advancing our understanding of spaceflight's impact on biological systems, ensuring humans will thrive in future deep space missions.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668403","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

The European Nucleotide Archive in 2024. 2024 年欧洲核苷酸档案。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2024-11-18 DOI: 10.1093/nar/gkae975

Colman O'Cathail, Alisha Ahamed, Josephine Burgin, Carla Cummins, Rajkumar Devaraj, Khadim Gueye, Dipayan Gupta, Vikas Gupta, Muhammad Haseeb, Maira Ihsan, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Kadhirvelu, Manish Kumar, Ankur Lathi, Rasko Leinonen, Jasmine McKinnon, Lili Meszaros, Joana Pauperio, Stephane Pesant, Nadim Rahman, Gabriele Rinck, Sandeep Selvakumar, Swati Suman, Yanisa Sunthornyotin, Marianna Ventouratou, Zahra Waheed, Peter Woollard, David Yuan, Ahmad Zyoud, Tony Burdett, Guy Cochrane

引用次数: 0

Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes. 复合物门户网站 2025：预测的人类复合物以及用于比较同源和旁系复合物的增强型可视化工具。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2024-11-18 DOI: 10.1093/nar/gkae1085

Sucharitha Balu, Susie Huget, Juan Jose Medina Reyes, Eliot Ragueneau, Kalpana Panneerselvam, Samantha N Fischer, Erin R Claussen, Savvas Kourtis, Colin W Combe, Birgit H M Meldal, Livia Perfetto, Juri Rappsilber, Georg Kustatscher, Kevin Drew, Sandra Orchard, Henning Hermjakob

{"title":"Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes.","authors":"Sucharitha Balu, Susie Huget, Juan Jose Medina Reyes, Eliot Ragueneau, Kalpana Panneerselvam, Samantha N Fischer, Erin R Claussen, Savvas Kourtis, Colin W Combe, Birgit H M Meldal, Livia Perfetto, Juri Rappsilber, Georg Kustatscher, Kevin Drew, Sandra Orchard, Henning Hermjakob","doi":"10.1093/nar/gkae1085","DOIUrl":"https://doi.org/10.1093/nar/gkae1085","url":null,"abstract":"The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated reference database for molecular complexes. It is a unifying web resource linking aggregated data on composition, topology and the function of macromolecular complexes from 28 species. In addition to significantly extending the number of manually curated complexes, we have massively extended the coverage of the human complexome through the incorporation of high confidence assemblies predicted by machine-learning algorithms trained on large-scale experimental data. The current content of the portal comprising 2150 human complexes has been augmented by 14 964 machine-learning (ML) predicted complexes from hu.MAP3.0. We have refactored the website to enable easy search and filtering of these different classes of protein complexes and have implemented the Complex Navigator, a visualisation tool to facilitate comparison of related complexes in the context of orthology or paralogy. We have embedded the Rhea reaction visualisation tool into the website to enable users to view the catalytic activity of enzyme complexes.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668263","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

Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation. 本质上无序的 RNA 结合图案合作催化 RNA 折叠并驱动相分离。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2024-11-18 DOI: 10.1093/nar/gkae1107

Annika Niedner-Boblenz, Thomas Monecke, Janosch Hennig, Melina Klostermann, Mario Hofweber, Elena Davydova, André P Gerber, Irina Anosova, Wieland Mayer, Marisa Müller, Roland Gerhard Heym, Robert Janowski, Jean-Christophe Paillart, Dorothee Dormann, Kathi Zarnack, Michael Sattler, Dierk Niessing

{"title":"Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation.","authors":"Annika Niedner-Boblenz, Thomas Monecke, Janosch Hennig, Melina Klostermann, Mario Hofweber, Elena Davydova, André P Gerber, Irina Anosova, Wieland Mayer, Marisa Müller, Roland Gerhard Heym, Robert Janowski, Jean-Christophe Paillart, Dorothee Dormann, Kathi Zarnack, Michael Sattler, Dierk Niessing","doi":"10.1093/nar/gkae1107","DOIUrl":"https://doi.org/10.1093/nar/gkae1107","url":null,"abstract":"RNA-binding proteins are essential for gene regulation and the spatial organization of cells. Here, we report that the yeast ribosome biogenesis factor Loc1p is an intrinsically disordered RNA-binding protein with eight repeating positively charged, unstructured nucleic acid binding (PUN) motifs. While a single of these previously undefined motifs stabilizes folded RNAs, multiple copies strongly cooperate to catalyze RNA folding. In the presence of RNA, these multivalent PUN motifs drive phase separation. Proteome-wide searches in pro- and eukaryotes for proteins with similar arrays of PUN motifs reveal a strong enrichment in RNA-mediated processes and DNA remodeling. Thus, PUN motifs are potentially involved in a large variety of RNA- and DNA-related processes by concentrating them in membraneless organelles. The general function and wide distribution of PUN motifs across species suggest that in an ancient 'RNA world' PUN-like motifs may have supported the correct folding of early ribozymes.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668389","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

PubChem 2025 update. PubChem 2025 更新。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2024-11-18 DOI: 10.1093/nar/gkae1059

Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A Shoemaker, Paul A Thiessen, Bo Yu, Leonid Zaslavsky, Jian Zhang, Evan E Bolton

{"title":"PubChem 2025 update.","authors":"Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A Shoemaker, Paul A Thiessen, Bo Yu, Leonid Zaslavsky, Jian Zhang, Evan E Bolton","doi":"10.1093/nar/gkae1059","DOIUrl":"https://doi.org/10.1093/nar/gkae1059","url":null,"abstract":"PubChem (https://pubchem.ncbi.nlm.nih.gov) is a large and highly-integrated public chemical database resource at NIH. In the past two years, significant updates were made to PubChem. With additions from over 130 new sources, PubChem contains >1000 data sources, 119 million compounds, 322 million substances and 295 million bioactivities. New interfaces, such as the consolidated literature panel and the patent knowledge panel, were developed. The consolidated literature panel combines all references about a compound into a single list, allowing users to easily find, sort, and export all relevant articles for a chemical in one place. The patent knowledge panels for a given query chemical or gene display chemicals, genes, and diseases co-mentioned with the query in patent documents, helping users to explore relationships between co-occurring entities within patent documents. PubChemRDF was expanded to include the co-occurrence data underlying the literature knowledge panel, enabling users to exploit semantic web technologies to explore entity relationships based on the co-occurrences in the scientific literature. The usability and accessibility of information on chemicals with non-discrete structures (e.g. biologics, minerals, polymers, UVCBs and glycans) were greatly improved with dedicated web pages that provide a comprehensive view of all available information in PubChem for these chemicals.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668525","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

Correction to 'Regulation of the androgen receptor by SET9-mediated methylation'. SET9 介导的甲基化对雄激素受体的调控 "的更正。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2024-11-18 DOI: 10.1093/nar/gkae1166

引用次数: 0

The Immune Epitope Database (IEDB): 2024 update. 免疫表位数据库（IEDB）：2024 年更新。

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2024-11-18 DOI: 10.1093/nar/gkae1092

Randi Vita, Nina Blazeska, Daniel Marrama, Sebastian Duesing, Jason Bennett, Jason Greenbaum, Marcus De Almeida Mendes, Jarjapu Mahita, Daniel K Wheeler, Jason R Cantrell, James A Overton, Darren A Natale, Alessandro Sette, Bjoern Peters

引用次数: 0