NUCLEIC ACIDS RESEARCH核酸研究
NUCLEIC ACIDS RESEARCH(英文缩写 NUCLEIC ACIDS RES),ISSN 0305-1048,eISSN 1362-4962,中文译名:核酸研究 是一本学术期刊。本页汇总该期刊的最新影响因子、分区信息以及最新收录于 PubMed 的文献,帮助您快速了解期刊全貌。
发文量统计区间：2025-11-01 至 2026-10-31，按本站收录文献的发表日期统计。
期刊介绍
历年影响因子趋势
| JCR 数据年份 | 影响因子 | JCR 分区 |
|---|---|---|
| 2021 | 19.160 | Q1 |
| 2022 | 14.900 | Q1 |
| 2023 | 16.600 | Q1 |
| 2024 | 13.100 | Q1 |
| 2025 | 15.000 | Q1 |
NUCLEIC ACIDS RESEARCH 最新收录文献
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1. PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN.
1. PanGBank：一个使用PPanGGOLiN构建的大规模预计算微生物泛基因组资源PMID:日期:2026-10-05PanGBank (https://pangbank.genoscope.cns.fr) is a comprehensive open-access database providing precomputed prokaryotic pangenomes at a broad taxonomic scale. Built upon PPanGGOLiN partitioned pangenome graphs, PanGBank addresses the growing need for large-scale comparative genomics through a standardized, regularly updated, and fully accessible resource. The initial release comprises two complementary collections covering >4600 prokaryotic species from the Genome Taxonomy Database (GTDB), encompassing over 393 000 genomes: GTDB_all, maximizing taxonomic and environmental diversity through the inclusion of metagenome-assembled genomes and single-cell amplified genomes, and GTDB_refseq, focusing on high-quality, annotation-rich genomes. Each species-level pangenome integrates graph-based statistical partitions into persistent, shell, and cloud gene families, together with regions of genomic plasticity (panRGP) and co-localized functional modules (panModule). PanGBank offers multiple access modes, including a REST API, a command-line interface, and an interactive web interface. By combining large-scale pangenome resources with advanced graph-based analyses, PanGBank provides a scalable framework for exploring microbial diversity, genome evolution, functional variation, and the dissemination of adaptive traits across prokaryotic populations, as illustrated by a use case on Acinetobacter baumannii pangenome investigating the distribution and evolution of antimicrobial resistance determinants.
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2. SingPro 2.0: a proteomics-centric knowledge base for single-cell multimodal profiling.
PMID:日期:2026-09-30Protein-inclusive single-cell multimodal profiling has emerged as a transformative strategy for resolving cellular heterogeneity by jointly measuring proteins and complementary molecular features in the same cells. The resulting protein-inclusive datasets are increasingly used to characterize cellular states, construct multimodal cell atlases, and decode disease mechanisms. However, such data are rarely included in existing databases. In this study, SingPro was updated from a single-cell proteomics database into a proteomics-centric knowledge base for single-cell multimodal profiling. Distinct from existing resources, the updated SingPro (a) systematically curates data and experimental details from 814 protein-inclusive multimodal studies encompassing ~81.5 million cells across 29 tissues, 44 diseases, and multiple species; (b) covers 5 omics modalities through 12 experimental technologies that simultaneously profile proteins with messenger RNA, chromatin accessibility, or other measurements in the same cell; and (c) provides cross-modality visualization for joint analysis. SingPro is freely accessible without requiring login or registration at: https://idrblab.org/singpro/.
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3. circRNADisease v3.0: an updated resource for high-quality, experimentally supported circRNA-disease associations.
PMID:日期:2026-09-25Systematic integration of circular RNA (circRNA)-disease associations is essential for elucidating the roles of circRNAs in disease pathogenesis and evaluating their potential as biomarkers and therapeutic targets. circRNADisease was established as a manually curated database of experimentally supported circRNA-disease associations. Here, we present circRNADisease v3.0, a substantially expanded and enhanced release containing 15 390 curated circRNA-disease entries involving 9168 circRNAs, 656 MONDO-standardized disease terms, and 66 species, representing more than a twofold increase in data volume compared with v2.0. Each record is assigned a confidence score according to the strength and diversity of supporting evidence, including clinical evidence, circular-transcript identity verification, expression detection, functional experiments, molecular-mechanism validation, and bioinformatic analysis. The updated database also incorporates genomic coordinates, subcellular localization, experimental validation methods, clinical significance, data and code availability, and cross-references to multiple disease terminologies. Two new modules have been introduced. Circ2CNV contains 2 962 504 circRNA-cancer cohort records with copy-number variations across 33 TCGA cancer cohorts, whereas Circ2Celltype comprises 2025 cell-type-resolved evidence records covering 29 cell types. Together with the existing Circ2Mut module, these additions connect literature-curated circRNA-disease associations with genomic alterations and cellular contexts. circRNADisease v3.0 provides a comprehensive and evidence-oriented platform for circRNA research and is freely available at http://cgga.org.cn/circRNADisease/.
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4. Mechanism of NanR transcriptional activation of sialic acid metabolism in Streptococcus pneumoniae.
4. 肺炎链球菌中NanR转录激活唾液酸代谢的机制PMID:日期:2026-09-22In Streptococcus pneumoniae, the RpiR transcriptional regulator NanR (SpNanR) senses sialic acid in the environment and upregulates transcription of the nan and sia A operons to increase uptake and metabolism of sialic acid. The molecular basis of this activation is unknown. Here, we demonstrate that SpNanR binds N-acetylmannosamine-6-phosphate, a metabolite of sialic acid catabolism. SpNanR exists in a dimer-tetramer equilibrium, and N-acetylmannosamine-6-phosphate binding strongly stabilizes the tetramer. Crystal structures and site-specific substitutions demonstrate that N-acetylmannosamine-6-phosphate bridges and stabilizes the SpNanR tetramer. SpNanR binds its DNA recognition sequence with nanomolar affinity. Notably, the effector N-acetylmannosamine-6-phosphate does not affect the affinity of SpNanR for DNA. The DNA-binding domains are not structurally coupled to the sugar isomerase domains, explaining why N-acetylmannosamine-6-phosphate binding does not affect DNA binding. Structural analysis reveals that sequence specificity arises through distortion of B-DNA and an unusual π-stack formed by two arginine residues in the minor groove, while affinity is driven by backbone contacts. We propose a mechanism by which S. pneumoniae regulates sialic acid metabolism, consistent with our biophysical experiments and in vivo regulatory behavior. These findings define a unique activation mechanism for an RpiR regulator and provide new insights into carbohydrate-responsive gene regulation in pneumococci.
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5. Structural basis of PARP2 recognition of nucleosomal DNA breaks and inhibitor trapping.
5. PARP2识别核小体DNA断裂和抑制剂捕获的结构基础PMID:日期:2026-09-22Single-strand DNA breaks are among the most frequent forms of DNA damage, yet how PARP2 recognizes these lesions within the constrained geometry of chromatin remains unclear. Here we use cryogenic electron microscopy (cryo-EM) to determine structures of PARP2 and HPF1 bound to nucleosomes containing a site-specific single-strand break (SSB) at superhelical location + 5.3. The structures reveal a multivalent binding mode in which the Trp-Gly-Arg (WGR) domain engages the break while the helical domain and HPF1 contact the opposing DNA gyre, spanning both DNA gyres of the nucleosome. This configuration explains the higher affinity of PARP2 for nucleosomal SSBs relative to free DNA. 3D classification resolves multiple PARP2-bound states with distinct WGR orientations and DNA backbone distortions, revealing structural plasticity during damage recognition. Comparative analysis shows that HPF1 constrains the conformational ensemble of PARP2 and promotes a defined catalytic domain architecture compatible with histone PARylation. PARP inhibitors (olaparib, talazoparib, EB-47) stabilize WGR-helical domain interfaces and make the ADP-ribosyltransferase-HPF1 catalytic module dynamic, consistent with reverse allosteric retention on damaged chromatin, while also promoting asymmetric nucleosomal DNA unwrapping. Together, these structures provide a chromatin-context framework for understanding PARP2 recognition of nucleosomal DNA breaks and how PARPis reshape these interactions to promote PARP retention and local chromatin remodeling.
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6. A systematic single-cell analysis of enhancer RNAs across human and mouse.
6. 对人类和小鼠增强子RNA的系统性单细胞分析PMID:日期:2026-09-22Enhancer RNAs (eRNAs) contribute to gene expression specificity, yet their expression patterns at single-cell resolution remain poorly understood. Across 184 329 high-quality single cells from 187 full-length single-cell RNA-seq datasets, we identified 85 977 human and 82 727 mouse eRNAs, which were sparsely detected at the single-cell level (<5% in humans and <8% in mice) but showed high intercellular heterogeneity and contributed substantially to lineage-specific marker repertoires, accounting for up to 33.5% of human and 46.5% of mouse lineage markers. Through systematic analysis of eRNA expression patterns in embryonic development, brain tissues, and cancer, cell-specific eRNAs in different cell types were identified and corresponding regulatory networks were constructed. Our results indicate that eRNAs play important roles in diverse biological processes through modulation of gene expression. Finally, RACE confirmed the full transcription of a colorectal cancer-associated eRNA, whose elevated plasma levels, diagnostic performance, and postoperative reduction support its potential as a noninvasive biomarker for colon cancer detection and monitoring. Collectively, this study provides a comprehensive single-cell landscape of eRNA expression and offers a valuable resource for understanding eRNA-mediated regulatory mechanisms.
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7. RMI2 regulates recombination intermediate metabolism to ensure proper chromosome segregation in mammalian meiosis.
PMID:日期:2026-09-22Proper segregation of meiotic chromosomes depends on the controlled formation and resolution of recombination intermediates that give rise to crossovers (COs). While the BTRR complex-comprising the BLM helicase, topoisomerase IIIα, and the proteins RMI1 and RMI2-is a well-characterized regulator of recombination in somatic cells, its function during meiosis remains incompletely understood, particularly for RMI2 in mammals. Here, we investigate the role of RMI2 in mouse spermatogenesis using a targeted RMI2 knockout model. Loss of RMI2 results in severe meiotic defects, including reduced testis size, increased apoptosis at the metaphase-anaphase I transition, and frequent chromosomal abnormalities such as lagging chromosomes in metaphase I cells and anaphase I chromatin bridges. Cytological analyses reveal disruptions in the processing of recombination intermediates. Our work monitoring molecular recombination outcomes at known recombination hotspots suggests that RMI2 regulates the balance of recombination pathways, constrains aberrant branch migration, and ensures proper CO maturation. Our findings show previously unappreciated functions for RMI2 essential for coordinating recombination intermediate metabolism and promoting proper chromosome conformation and segregation during meiosis. These results provide insights into the complex regulation of recombination intermediate homeostasis in higher eukaryotes and highlight the role of RMI2 in maintaining genome stability and proper gamete development in mammals.
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8. Size and sequence variation of the Lid of the Cas12a nuclease domain results in a nickase phenotype.
8. Cas12a核酸酶结构域Lid的大小和序列变异导致切口酶表型PMID:日期:2026-09-22CRISPR-Cas12a nucleases typically induce double-strand breaks (DSBs) to initiate genome editing. However, reliance on DSBs risks chromosomal rearrangements and unintended insertions or deletions at off-target sites. Therefore, engineering nickase variants that cleave only a single DNA strand might enable precise editing platforms. We describe an unbiased in vivo screen in Escherichia coli to identify LbCas12a nickase variants. We targeted the RuvC Lid domain for mutagenesis, hypothesizing that altering this region would disrupt the coordination of strand cleavage. While the screen produced many nickase variants with targeted point substitutions (Lid1), it also serendipitously yielded a variant (Lid2) with an unprecedented Lid domain in terms of size and sequence. Biochemical characterization confirms that Lid2 robustly nicks the non-target strand (NTS) with minor cleavage activity observed for the target strand (TS), accumulating predominantly nicked substrates. Cryo-electron microscopy (cryo-EM) at 2.5 Å resolution reveals that, in Lid2, the native α-helical Lid is replaced, uncoupling the concerted cleavage mechanism. Specifically, the remodeled Lid appears to stabilize the NTS in the active site, whereas it hampers the conformational transitions required for subsequent TS cleavage. This robust nickase-phenotype of this Cas12a variant expands the CRISPR-Cas toolbox and offers a new component for precise genome editing applications.
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9. Functional roles for viral RNA ribosylation in mammalian cells.
9. 病毒RNA核糖基化在哺乳动物细胞中的功能作用PMID:日期:2026-09-22In mammalian cells, the addition of ADP-ribose to proteins and DNA plays well established roles in regulating cell function. Recently, RNA ribosylation was also found in mammalian cells under conditions of cell stress, though the functional consequences remain unclear. Here we find that infection with chikungunya virus, a positive strand RNA virus that causes frequent widespread epidemics, increases overall levels of RNA ribosylation in human fibroblasts. During infection, viral RNA is ribosylated by the PARP12 ribosyltransferase, which is counteracted by the viral nsP3 ribosylhydrolase. Increased viral RNA ribosylation resulted in decreased translation in cell-free systems and infected fibroblasts, and more rapid viral RNA decay. Further, ribosylated RNA potently induced the expression of antiviral host response genes. Together these data show the first functional consequences of RNA ribosylation in mammalian cells by showing that RNA ribosylation inhibits translation, decreases RNA stability, and creates a novel pathogen-associated molecular pattern that activates the host innate immune response. As macrodomains are present in multiple unrelated viruses, our data suggest RNA ribosylation is a novel component of cellular antiviral sensing pathway. These results define a framework for understanding how RNA ribosylation regulates RNA metabolism during viral infection.