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Roles of dimeric intermediates in RNA-catalyzed rolling circle synthesis Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-16 Emil L Kristoffersen, Ewan K S McRae, Niels R Sørensen, Philipp Holliger, Ebbe S Andersen
The RNA world hypothesis is supported by the discovery of RNA polymerase ribozymes that can perform RNA-catalyzed RNA replication processes on different RNA templates. Recently, RNA-catalyzed rolling circle synthesis (RCS) on small circular RNA (scRNA) templates has been demonstrated. However, the structural and dynamic properties of scRNA replication and its products and intermediates have not been
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An endogenous retroviral element co-opts an upstream regulatory sequence to achieve somatic expression and mobility Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-16 Natalia Rubanova, Darshika Singh, Louis Barolle, Fabienne Chalvet, Sophie Netter, Mickaël Poidevin, Nicolas Servant, Allison J Bardin, Katarzyna Siudeja
Retrotransposons, multi-copy sequences that propagate via copy-and-paste mechanisms, occupy large portions of eukaryotic genomes. A great majority of their manifold copies remain silenced in somatic cells; nevertheless, some are transcribed, often in a tissue-specific manner, and a small fraction retains its ability to mobilize. While it is well characterized that retrotransposon sequences may provide
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Impact of a single 8-oxoguanine lesion on Watson–Crick and Hoogsteen base pair hybridization in telomeric DNA quantified using single-molecule force spectroscopy Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-16 Yuanlei Cheng, Ximin Wang, Xuyang Yang, Yashuo Zhang, Huijuan You
8-Oxoguanine (8-oxoG) is a common DNA oxidative lesion prevalent in telomeric regions. However, the impact of 8-oxoG modification on the Watson–Crick base pairing energy remains controversial, potentially due to the formation of partially folded intermediates. Here, we used single-molecule magnetic tweezers to characterize the mechanical stability and equilibrium folding/unfolding transitions of human
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The intrinsic preference of guanosine bases for cleavage-facilitating interactions with phosphodiester moieties in RNA anions revealed by base modifications and mass spectrometry Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-16 Anna Ploner, Christoph Mitteregger, Heidelinde Glasner, Raphael Bereiter, Ronald Micura, Kathrin Breuker
Spontaneous backbone cleavage of ribonucleic acids (RNAs) in basic aqueous solution has a preference for the 5′ side of guanosine. This phenomenon can also be observed in fully desolvated RNA (M − nH)n− ions subjected to vibrational activation by low-energy collisionally activated dissociation. However, the underlying chemical mechanism of the cleavage reaction has so far remained elusive. Using RNA
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Conserved long-range interactions are required for stable folding of orthoflaviviral genomic RNA Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-16 Michael Z Palo, Betty Ha, Christopher P Lapointe, Carlos Alvarado, John Janetzko, Jan E Carette, Joseph D Puglisi, Elisabetta Viani Puglisi
Long-range tertiary interactions are a widespread structural feature in viral RNAs (vRNAs) and mRNAs. In the orthoflaviviruses, conserved complementary sequences in the 5′ and 3′ terminal regions have an essential role in viral replication. Long-range pairing of these conserved sequences is proposed to facilitate a switch between two alternative vRNA conformations. Yet the detailed nature of these
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A flexible, high-throughput system for studying live mRNA translation with HiBiT technology Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-16 Camilla Ascanelli, Elsa Lawrence, Christopher A P Batho, Catherine H Wilson
HiBiT is an engineered luciferase’s 11-amino-acid component that can be introduced as a tag at either terminus of a protein of interest. When the LgBiT component and a substrate are present, HiBiT and LgBiT dimerize forming a functional luciferase. The HiBiT technology has been extensively used for high-throughput protein turnover studies in cells. Here, we have adapted the use of the HiBiT technology
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Nat10 maintains the homeostasis of pluripotent and 2-cell-like states in mouse embryonic stem cells through mRNA cytidine acetylation Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-16 Guofeng Feng, Guoxing Yin, Yusheng Liu, Chang Liu, Jie Li, Jiangtao Lu, Yongqin Yu, Ziyi Jin, Yiwei Wu, Yanbin Yue, Xiufang Gao, Jiaqiang Wang, Falong Lu, Lin Liu
Naïve mouse embryonic stem cells (mESCs) are characterized by a mixed population of cells in an interconvertible pluripotent state and a totipotent 2-cell (2C)-like state. It remains to be understood how the pluripotent state is maintained while the 2C-like state is suppressed. We show that N-acetyltransferase 10 (Nat10) maintains the pluripotent state and suppresses the 2C-like state in mESCs through
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Methylation of mycovirus DNA is mediated by the RNAi machinery in vegetative hyphae of Fusarium graminearum Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-16 Yanfei Wang, Wei Chen, Lihang Zhang, Shuangchao Wang, Jin-Rong Xu, Lihua Guo
DNA cytosine methylation is an important epigenetic mechanism for transposon silencing and gene regulation in fungi, particularly during sexual reproduction. However, its occurrence in vegetative hyphae and role in defense against mycoviruses is unclear. In this study, we demonstrated that genomic-wide cytosine methylation of the tripartite genomovirus FgGMTV1 occurs in the hyphae of Fusarium graminearum
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Efficient coordination between the winged helix domain and the aromatic-rich loop restructures the ATPase domain and facilitates DNA unwinding by human RECQ1 Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-13 Tulika Das, Swagata Mukhopadhyay, Amit K Das, Agneyo Ganguly
RecQ helicases can unwind a wide spectrum of DNA structures and thereby protect the cells from genome instability. Unwinding mechanisms have been extensively studied for bacterial and human RecQ helicases. DNA-induced winged helix (WH) domain repositioning and allosteric remodeling of the ATPase domain have been shown to be important for unwinding activity of bacterial RecQ helicases. In contrast,
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Super-enhancer-mediated circRNAs exhibit high splicing circularization diversity and transcriptional activity Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-13 Shaodong Huang, Yulong Han, Yiran Liu, Lina Bu, Chenyang Wu, Ziyan Rao, Chuan Ye, Hansen Cheng, Yunxi Liao, Yunan Sun, Yushu Zou, Zixu Wang, Bryan-Yu Sun, Shu Meng, Dongyu Zhao
Circular RNAs (circRNAs), an emerging subclass of noncoding RNAs, have been increasingly recognized as critical regulators in diverse biological functions and cellular processes. Despite their functional significance, the epigenetic mechanisms governing circRNA biogenesis remain poorly understood. Our study reveals that H3K27ac-marked super-enhancers (SEs) significantly enhance both circRNA splicing
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Unraveling the regulatory dynamics of bidirectional promoters for modulating gene co-expression and metabolic flux in Saccharomyces cerevisiae Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-12 Zimo Jin, Yueming Dong, Abdul Muntakim Rafi, Md Mohsin Patwary, Catherine Xu, Morten H Raadam, Carl G de Boer, Codruta Ignea
Bidirectional promoters (BDPs) hold great promise for applications in synthetic biology by enabling co-expression of multiple genes with minimized promoter size. However, the lack of well-characterized BDPs along with an incomplete understanding of their regulatory mechanisms limits broader applications. Here, we conducted genome-wide screening and characterization of 749 BDP candidates containing
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Phosphorylation of the protamine-like protein from baculovirus affects its DNA binding and virus propagation Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-12 Qian Cheng, Siqi Zhu, Yanrong Lv, JiongJiong Liu, Qinglin Su, Meijin Yuan, Yang Liu, Kai Yang
Viral DNA-binding proteins, a type of protamine-like protein, pack the viral genome and promote late viral gene expression. In baculovirus Autographa californica multiple nucleopolyhedrovirus, DNA-binding protein P6.9 plays a crucial role in the production of progeny viruses. Earlier studies suggested the importance of P6.9 phosphorylation states in its function, while the detailed mechanism remains
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The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-12 Hugh K Haddox, Georg Angehrn, Luca Sesta, Chris Jennings-Shaffer, Seth D Temple, Jared G Galloway, Angie S Hinrichs, William S DeWitt, Jesse D Bloom, Frederick A Matsen IV, Richard A Neher
RNA viruses like SARS-CoV-2 have high mutation rates, which contribute to their rapid evolution. Mutation rates depend on mutation type and can vary between sites in a virus’s genome. Understanding this variation can shed light on the mutational processes at play, and is crucial for quantitative modeling of viral evolution. Using millions of SARS-CoV-2 full-genome sequences, we estimate rates of synonymous
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KIF2C condensation concentrates PLK1 and phosphorylated BRCA2 on kinetochore microtubules in mitosis Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-11 Anastasiia Skobelkina, Manon Julien, Sylvain Jeannin, Simona Miron, Tom Egger, Rady Chaaban, Guillaume Bouvignies, Emile Alghoul, Rania Ghouil, Claire Friel, Didier Busso, Juan C Cañas, François-Xavier Theillet, Romain Le Bars, Aura Carreira, Angelos Constantinou, Jihane Basbous, Sophie Zinn-Justin
During mitosis, the microtubule depolymerase KIF2C, the tumor suppressor BRCA2, and the kinase PLK1 contribute to the control of kinetochore-microtubule attachments. Both KIF2C and BRCA2 are phosphorylated by PLK1, and BRCA2 phosphorylated at T207 (BRCA2-pT207) serves as a docking site for PLK1. Reducing this interaction results in unstable microtubule-kinetochore attachments. Here we identified that
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A temperature-driven DNA discrimination strategy to distinguish E. coli DNA and phage 5hmC-modified DNA Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-11 Yue Kang, Yahui Liu, Haolong Zhou, Biyun Ma, Huan Chen, Kaining Zhang, Yawen Wang, Chengpeng Fan, Huaiyu Yang, Yingqi Xu, Steve Matthews, Shuai Yuan, Yan Li, Bing Liu
The arms race between phages and bacteria is dynamic and ongoing, with both continuously acquiring new strategies to outcompete each other during co-evolution. Here, we report bacteriophage T4 exonuclease DexA and an uncharacterized Escherichia coli exonuclease as a rare pair of attack and defense duo arising from the same mechanism. DexA, highly conserved among phages, has two well-characterized biological
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Structurally distinct manganese-sensing riboswitch aptamers regulate different expression platform architectures Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-11 Christine Stephen, Danea E Palmer, Clarisa Bautista, Tatiana V Mishanina
Manganese (Mn)-sensing riboswitches protect bacteria from Mn toxicity by upregulating expression of Mn exporters. The Mn aptamers share key features but diverge in other important elements, including within the metal-binding core. Although X-ray crystal structures of isolated aptamers exist, these structural snapshots lack crucial details about how the aptamer communicates the presence or absence of
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The mammalian Ku70 C-terminus SAP domain is required to repair DNA damage Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-11 Yuan Wang, Michael S Czap, Hailey Kim, Paul M Masaka, Hongxin Wang, Md Amjad Beg, Huimei Lu, Jingmei Liu, Yoke-Chen Chang, Peter J Romanienko, Cristina Montagna, Zhiyuan Shen
The mammalian non-homologous end joining (NHEJ) is required for class switch and V(D)J recombination as well as repairing DNA double-strand breaks (DSBs). Initiated by the binding of Ku70/Ku80 (Ku) dimer to DNA ends and the recruitment of the DNA-dependent protein kinase catalytic subunit, NHEJ plays a key role in DSB repair. While the overall function of Ku70 in NHEJ is well documented, the specific
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Deciphering the role of accessory proteins in Arabidopsis chloroplast editosomes via interaction with a synthetic PPR-PLS factor in E. coli Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-11 Jose M Lombana, Maureen R Hanson, Stéphane Bentolila
RNA editing modifies cytidines to uridines in plant organelle transcripts so that their sequences differ from the ones predicted from the genomic DNA. This process involves a family of RNA-binding proteins that has significantly expanded, the pentatricopeptide repeat (PPR)-containing proteins. In angiosperms, PPR proteins are found in editosomes associated with accessory proteins. The exact function
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R-2-hydroxyglutarate-mediated inhibition of KDM4A compromises telomere integrity Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-11 Florence Couteau, Laurence M Gagné, Karine Boulay, Philippe Rousseau, Mélissa Carbonneau, Mary McQuaid, Jyoti Sharma, Christina Sawchyn, Erlinda Fernandez, Dagmar Glatz, Rana Rizk, Marie-Eve Lalonde, Yosra Mehrjoo, Tsz Wai Chu, Gaël Moquin-Beaudry, Christian Beauséjour, Mikhail Sergeev, Santiago Costantino, Daina Avizonis, Ivan Topisirovic, Nada Jabado, Hugo Wurtele, Chantal Autexier, Frédérick A Mallette
Mutation, deletion, or silencing of genes encoding cellular metabolism factors occurs frequently in human malignancies. Neomorphic mutations in isocitrate dehydrogenases 1 and 2 (IDH1/2) promoting the production of R-2-hydroxyglutarate (R-2HG) instead of α-ketoglutarate (αKG) are recurrent in human brain cancers and constitute an early event in low-grade gliomagenesis. Due to its structural similarity
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Configuration of adaptable template RNA architectures to unfold the editable space of a nuclease prime editor Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-11 Pingbo Chen, Xiangyang Li, Qian Zhou, Jingzhou Chen, Lijin Lu, Pei Wang, Guiquan Zhang, Dongxiao Sun, Xingxu Huang, Jianghuai Liu, Xiaolong Wang
The nuclease prime editor (PEn) combines double-strand break (DSB) induction with reverse transcription for editing. Recently, high-activity PEn forms (e.g. uPEn) have been developed via the concomitant application of DNA repair regulator(s). While the standard uPEn introduces edits only downstream of the nuclease-induced DNA break, we seek innovative designs to enable upstream-directed editing by
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Boosting CRISPR/Cas12a intrinsic RNA detection capability through pseudo hybrid DNA–RNA substrate design Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-11 Jie Qiao, Junqi Zhang, Qingyuan Jiang, Shuqi Jin, Ruyi He, Bin Qiao, Yi Liu
The CRISPR/Cas12a [clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 12a] system is known for its intrinsic RNA-guided trans-cleavage activity; however, its RNA detection sensitivity is limited, with conventional methods typically achieving detection limits in the nanomolar range. Here, we report the development of a “pseudo hybrid DNA–RNA” (PHD) assay that significantly
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Asymmetric loading of TnsE regulates Tn7 targeting of DNA replication structures Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-11 Shreya S Krishnan, Yao Shen, Treasa B O’Hagan, Lindsay A Matthews, Nuwani W Weerasinghe, Rodolfo Ghirlando, Christopher J Thibodeaux, Alba Guarné
Tn7 transposable elements are known for their sophisticated target-site selection mechanisms. For the prototypical Tn7 element, dedicated transposon-encoded proteins direct insertions to either a conserved site in the chromosome or replicating DNA structures in conjugal plasmids, ensuring the vertical and horizontal spread of the element. While the pathway targeting the attTn7 site in the bacterial
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VimR is a conserved master transcription regulator controlling virulence and metabolism in Pseudomonas Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-11 Fang Chen, Yue Sun, Jiadai Huang, Tianmin Li, Beifang Lu, Zhe He, Jingwei Li, Tianqi Wang, Haiyan Hu, Xin Deng
Pseudomonas syringae, a highly destructive plant bacterial pathogen causing severe disease and significant yield losses in agriculture globally, has complex regulatory systems involving many transcriptional factors (TFs). Although the LysR-type transcriptional regulator (LTTR) protein family is a well-known group of TFs involved in diverse physiological functions, the roles of LTTRs in P. syringae
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Visualizing the transcription and replication of influenza A viral RNAs in cells by multiple direct RNA padlock probing and in situ sequencing (mudRapp-seq) Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-09 Shazeb Ahmad, Jianhui Li, Joél Schaust, Anne-Sophie Gribling-Burrer, Nina Geiger, Sabine C Fischer, Uddhav B Ambi, Simone Backes, Markus J Ankenbrand, Redmond P Smyth
Influenza A viruses (IAVs) contain eight negative-sense single-stranded viral RNA (vRNA) molecules, which are transcribed into messenger RNA (mRNA) and replicated via complementary RNA (cRNA). These processes are tightly regulated, but the precise molecular mechanisms governing the switch from transcription to replication remain elusive. Here, we introduce multiple direct RNA-assisted padlock probing
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Deciphering meiotic chromatin organization by SYCP3 Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-09 Shimeng Guo, Yiran Zhang, Caifeng Fei, Xiaozhao Liu, Wei Xia, Mengcheng Luo, Gonghong Wei, Weibing Qin, Chengliang Xiong, Honggang Li, Ying Yin, Ximiao He, Li-quan Zhou
Chromatin structure during meiosis is different from somatic cells due to the assembly of the synaptonemal complex between homologous chromosome axes. However, genome-wide organizing principles of this meiosis-specific multiprotein complex remain mysterious despite intensive super-resolution imaging analysis. Here, we profiled chromatin occupancy of SYCP3, the key chromatin organizer of synaptonemal
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Observing nucleotide flipping in DNA using indirect 2′-F nucleotide probes and 19F NMR Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-09 Lakshmi S Pidugu, Erin E Gustafson, Hardler W Servius, Mary E Cook, Nina C Lee, Kristen M Varney, Alexander C Drohat
Many proteins that bind specifically to DNA and RNA employ a mechanism known as nucleotide flipping, whereby a nucleotide rotates out of the helical stack and into an active site. This conformational change can be monitored using spectroscopic methods, including fluorescence and nuclear magnetic resonance (NMR). We previously showed that flipping of a 2′-fluoroarabino-substituted nucleotide by thymine
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Kinetic analysis and engineering of thermostable Cas12a for nucleic acid detection. Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-06 Juan Pan,Megumu Mabuchi,Daniel W Kneller,Ryan T Fuchs,Jennifer L Curcuru,Esta Tamanaha,Nathan A Tanner,G Brett Robb,Ivan R Corrêa
Cas12a trans nuclease activity has been leveraged for nucleic acid detection, often coupled with isothermal amplification to increase sensitivity. However, due to the lack of highly efficient thermostable Cas12a orthologs, use of Cas12a in one-pot combination with high temperature (55-65°C) amplification, such as loop-mediated isothermal amplification (LAMP), has remained challenging. Here, we attempt
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Genome-wide maps of UV damage repair and mutation suppression by CPD photolyase. Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-06 Kaitlynne A Bohm,Marian F Laughery,Piotr A Mieczkowski,Steven A Roberts,John J Wyrick Data Curation
Ultraviolet (UV) light causes cyclobutane pyrimidine dimers (CPDs) and other DNA lesions that must be efficiently repaired to prevent cell death and mutagenesis. While mammals utilize the nucleotide excision repair (NER) pathway to repair CPDs, many species primarily utilize photolyase enzymes to repair UV damage. Our understanding of how different genomic and chromatin features impact photolyase repair
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The functionality of telomerase depends on CPF-CF induced 3'end processing of its RNA component TLC1 and a novel Nrd1-Nab3 surveillance mechanism. Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-06 Jan-Philipp Lamping,Heike Krebber
Telomere elongation is driven by telomerase, which consists of several proteins and the ncRNA component TLC1 in yeast. While many ncRNAs are terminated via the Nrd1-Nab3-Sen1 (NNS) pathway, we found that TLC1 requires cleavage and polyadenylation factor (CPF)-cleavage factor (CF) mediated 3'end processing and the resulting poly(A) tail to mature into a functional ribozyme. The poly(A) tail is predicted
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Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch–probe arrays Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-06 Timothy K Chiang, Ofer Kimchi, Herman K Dhaliwal, Daniel A Villarreal, Fernando F Vasquez, Vinothan N Manoharan, Michael P Brenner, Rees F Garmann
We describe a DNA-array-based method to infer intramolecular connections in a population of RNA molecules in vitro. First we add DNA oligonucleotide “patches” that perturb the RNA connections, and then we use a microarray containing a complete set of DNA oligonucleotide “probes” to record where perturbations occur. The pattern of perturbations reveals couplings between regions of the RNA sequence,
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Bacterial RecD2 is a processive single-stranded DNA translocase with strand-switching capacity at DNA forks Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-06 Silvia Hormeño, Cristina Ramos, Javier Mendia-Garcia, Clara Aicart-Ramos, Silvia Ayora, Fernando Moreno-Herrero
RecD2 is a superfamily 1B helicase involved in DNA replication and repair, modulating replication restart, fork progression, and RecA recombinase activity. In this work, we have characterized the functions of Bacillus subtilis RecD2 using biochemical and single-molecule approaches. ATPγS binding and low MgCl2 concentrations enhance DNA association, with a preference for forked structures and unstructured
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The low endoribonuclease activity and lack of rNMP preference of human mitochondrial topoisomerase 1 protect against ribonucleotide-dependent deletions Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-06 Cyrielle P J Bader, Erika Miyazaki-Kasho, Josefin M E Forslund, Aiswarya Dash, Malgorzata Wessels, Paulina H Wanrooij
The incorporation of ribonucleotides (rNMPs) into the nuclear genome leads to severe genomic instability, including strand breaks and short 2–5 bp deletions at repetitive sequences. Curiously, the detrimental effects of rNMPs are not observed for the human mitochondrial genome (mtDNA) that typically contains several rNMPs per molecule. Given that the nuclear genome instability phenotype is dependent
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p53 reveals principles of chromatin remodeling and enhancer activation Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-06 Martin Fischer, Robert Schwarz, Konstantin Riege, Silke Förste, Katjana Schwab, Elina Wiechens, Alena van Bömmel, Steve Hoffmann
Pioneer transcription factors can bind to closed chromatin, initiating its opening and subsequent gene activation. However, the specific features that enable transcription factors to activate particular loci remain largely undefined. Here, we show that the transcription factor p53 unexpectedly initiates epigenetic remodeling at the majority of its binding sites and drives transcription at select loci
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Genome rearrangements induced by the stimulation of end-joining of DNA double strand breaks through multiple phosphorylation of MRE11 by the kinase PKB/AKT1 Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-06 Josée Guirouilh-Barbat, Iman Litchy Boueya, Camille Gelot, Gaëlle Pennarun, Christine Granotier-Beckers, Elodie Dardillac, Wei Yu, Chloé Lescale, Emilie Rass, Olivier Ariste, Nicolas Siaud, Benjamin Renouf, Armel Millet, Nadine Puget, Pascale Bertrand, Pierre de la Grange, Erika Brunet, Ludovic Deriano, Bernard S Lopez
Genetic instability is a major hazard threatening the fate of cells and ultimately of organisms. DNA double-strand break (DSB) is a highly toxic lesion, jeopardizing genome stability. Using cytogenetic and differential exome sequencing, we show here that upregulation of the kinase PKB/AKT1 leads to genomic rearrangements and chromosome fusions. By combining various approaches, at the genome scale and
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Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-06 Krystal A Orlando, Sara A Grimm, Paul A Wade
Pioneer transcription factors (PTFs) bind to inaccessible chromatin and recruit collaborating transcription factors to promote chromatin accessibility. However, mechanisms driving PTFs to specify collaborating transcription factor recruitment and chromatin remodeling remain unclear. Here, we utilize inducible expression of a PTF, GATA3, in a basal breast cancer cell line (SUM159PT) to mechanistically
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Selective engineering of condensation properties of single-stranded DNA binding (SSB) protein via its intrinsically disordered linker region Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-06 Péter Ecsédi, Dávid Érfalvy, Zoltán J Kovács, Viktoria Katran, János Pálinkás, Miklós Cervenak, Rita Pancsa, Gábor M Harami, László Smeller, Mihály Kovács
Single-stranded DNA binding (SSB) proteins are essential components of genome metabolism in both bacteria and eukaryotes. Recently demonstrated condensation propensities have placed SSB functions in a new context regarding the organization of nucleic acid-modifying complexes. In this work, we provide functional dissection of the condensation and partner binding properties of Escherichia coli (Ec) SSB
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Unlocking the serine mischarging paradox and inhibiting lactyltransferase activity of AlaRS by a single-point mutation Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-06 Wooyoung Park, Se-Young Son, Joonyeop Yi, Seungwoo Cha, Hankyeol Moon, Minyoung Kim, Sangho Ji, Wookyung Yu, Changmin Sung, Sun-Shin Cha, Ji-Sook Hahn
Aminoacyl-tRNA synthetases are critical for accurate genetic translation, attaching amino acids to their corresponding transfer RNA molecules. Alanyl-tRNA synthetase (AlaRS) often misactivates Ser or Gly instead of Ala, which is detrimental unless corrected by its editing functions. The paradox of misactivating larger Ser by AlaRS was considered inevitable due to its inherent design, sharing an essential
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A role for pH dynamics regulating transcription factor DNA-binding selectivity Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-04 Kyle P Kisor, Diego Garrido Ruiz, Matthew P Jacobson, Diane L Barber
Intracellular pH (pHi) dynamics regulates diverse cell processes such as proliferation, dysplasia, and differentiation, often mediated by the protonation state of a functionally critical histidine residue in endogenous pH sensing proteins. How pHi dynamics can directly regulate gene expression or whether transcription factors can function as pH sensors has received limited attention. We tested the
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Structural and functional characterization of human SLFN14 Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-04 Meng Luo, Xudong Jia, Zi-Wen Wang, Jin- Yu Yang, Wen Wang, Jiazhen Chen, Jun-Ying Ou, Jian-Xiong Feng, Bing Yu, Sheng Wang, Lin Huang, Neil V Morgan, Kai Deng, Tongsheng Chen, Qinfen Zhang, Song Gao
The Schlafen (SLFN) family of proteins are a group of DNA/RNA processing enzymes with emerging importance in human health and disease, where their functions are implicated in a variety of immunological and anti-tumor processes. Here, we present the cryo-electron microscopy structure of full-length human SLFN14, a member with antiviral activity and linked to an inherited bleeding disorder. SLFN14 is
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An antibiotic-responsive regulator orchestrates chronic-to-acute virulence switch in Pseudomonas aeruginosa Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-04 Xinbo Wang, Guizhen Li, Yuzheng Zou, Huiluo Cao, Lisheng Liao, Xiaofan Zhou, Lian-Hui Zhang, Zeling Xu
Misuse and overuse of antibiotics have led to the rapid emergence of antibiotic-resistant superbugs. In addition, evidence is emerging that antibiotic exposure could impose substantial influence on bacterial virulence, but the underlying mechanisms remain poorly understood. Here, we discovered a highly conserved aminoglycoside-responsive regulator, AmgR, that inversely modulates the production of destructive
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Diffdigester.uni-jena.de: a tool for optimized selection of restriction enzymes for plasmid identification in cloning procedures Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-04 Martin Gühmann, Stefanie Reuter, Ralf Mrowka
Differential digests, also known as test or diagnostic digests, are a standard method in molecular cloning to verify whether a picked clone is indeed the target plasmid or not. However, finding the optimal restriction enzyme for a differential digest by hand may be challenging and time-consuming. To address this problem, we created diffdigester.uni-jena.de (https://diffdigester.uni-jena.de), a free
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Compromised two-start zigzag chromatin folding in immature mouse retina cells driven by irregularly spaced nucleosomes with short DNA linkers Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-04 Brianna Kable, Stephanie Portillo-Ledesma, Evgenya Y Popova, Nathan Jentink, Matthew Swulius, Zilong Li, Tamar Schlick, Sergei A Grigoryev
The formation of condensed heterochromatin is critical for establishing cell-specific transcriptional programs. To reveal structural transitions underlying heterochromatin formation in maturing mouse rod photoreceptors, we apply cryo-electron microscopy (cryo-EM) tomography, AI-assisted denoising, and molecular modeling. We find that chromatin isolated from immature retina cells contains many closely
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Single-cell imaging of N4-acetylcytidine-modified RNA using fluorine metabolic labeling mediated proximity ligation assay Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-04 Qi Wang, Yuhao Du, Shen Yan, Ziang Lu, Yongling Tang, Feng Xiao, Fuling Zhou, Xiang Zhou
N 4-Acetylcytidine (ac4C) is an emerging epitranscriptomic mark involved in regulating RNA stability, translation, and gene expression. Despite its emerging role in gene regulation and disease, current methods for in situ detection of ac4C-modified RNA lack sensitivity and specificity. To overcome these challenges, we developed fluorine metabolic labeling mediated proximity ligation assay (FMPLA),
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A post-assembly conformational change makes the SARS-CoV-2 polymerase elongation-competent Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-04 Misha Klein, Arnab Das, Subhas C Bera, Thomas K Anderson, Dana Kocincova, Hery W Lee, Bing Wang, Flavia S Papini, John C Marecki, Jamie J Arnold, Craig E Cameron, Kevin D Raney, Irina Artsimovitch, Mathias Götte, Robert N Kirchdoerfer, Martin Depken, David Dulin
Coronaviruses (CoVs) encode 16 nonstructural proteins (nsps), most of which form the replication–transcription complex (RTC). The RTC contains a core composed of one nsp12 RNA-dependent RNA polymerase (RdRp), two nsp8s, and one nsp7. The core RTC recruits other nsps to synthesize all viral RNAs within the infected cell. While essential for viral replication, the mechanism by which the core RTC assembles
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The mechanism of lineage-specific tRNA recognition by bacterial tryptophanyl-tRNA synthetase and its implications for inhibitor discovery Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-04 Xiaoying Peng, Kaijiang Xia, Lingzhen Xiao, Haoran Qi, Qingting Huang, Manli Xiang, Lu Han, Haipeng Qiu, Qiong Gu, Bingyi Chen, Huihao Zhou
Tryptophanyl-tRNA synthetase (TrpRS) catalyzes the attachment of tryptophan (l-Trp) to tRNATrp, thereby providing the ribosome with a crucial substrate for the decoding of the UGG codon during protein translation. Both bacterial and eukaryotic TrpRSs are unable to efficiently cross-aminoacylate their respective tRNATrp substrates, indicating the evolution of lineage-specific mechanisms for tRNATrp
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Structural and molecular mechanisms of an Ro60 homolog from a Thermus bacteriophage Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-04 Zetao Hu, Zhaohui Jin, Lulu Guo, Ling Zeng, Xuanjia Dong, Lin Jiang, Wenting Dai, Jinbiao Ma, Ying Huang
Ro60 is a conserved RNA-binding protein essential for RNA quality control and implicated in autoimmune responses. In this study, we present the structural and functional characterization of φRo60, an Ro60 homolog from Thermus phage phiLo, with its crystal structure determined at 1.99 Å. Despite limited sequence identity with bacterial and amphibian homologs, φRo60 maintains the canonical doughnut-shaped
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In vivo single-molecule imaging of RecB reveals efficient repair of DNA damage in Escherichia coli Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-04 Alessia Lepore, Daniel Thédié, Lorna McLaren, Louise Goossens, Benura Azeroglu, Oliver J Pambos, Achillefs N Kapanidis, Meriem El Karoui
Efficient DNA repair is essential for maintaining genome integrity and ensuring cell survival. In Escherichia coli, RecBCD plays a crucial role in processing DNA ends, following a DNA double-strand break (DSB), to initiate repair. While RecBCD has been extensively studied in vitro, less is known about how it contributes to rapid and efficient repair in living bacteria. Here, we use single-molecule
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Haplotypic resolution of the challenging genomic regions of MHC and KIR using a combination of targeted sequencing and a novel assembly pipeline Nucleic Acids Res. (IF 16.6) Pub Date : 2025-06-04 Timothy L Mosbruger, Amalia Dinou, Jamie L Duke, Deborah Ferriola, Yang Li, Tristan J Hayeck, Dimitri S Monos
Recently long-read sequencing technologies and bioinformatics have enabled the construction of haplotype-resolved genome assemblies. Here, we present the complete and accurate de novo characterization of two challenging genomic regions, the major histocompatibility complex (MHC) and Killer-cell immunoglobulin-like receptors (KIRs), in phased haplotypic form, using the Oxford Nanopore Technology (ONT)
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Screening of metallohelices for enantioselective targeting SARS-CoV-2 RNA G-quadruplex Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-31 Yue Sun, Chuanqi Zhao, Yan Liu, Yibo Wang, Cheng Zhang, Jie Yang, Geng Qin, Hualong Song, Miles Postings, Peter Scott, Jinsong Ren, Xiaogang Qu
The emergence of numerous variants of SARS-CoV-2 still presents the major challenges in the fight against this disease by reducing the efficacy of vaccines and drugs. RNA G-quadruplexes (G4s) in the SARS-CoV-2 genome are highly conserved and have thus been spotlighted as a promising therapeutic target to combat a wider range of variants. However, very few RNA G4 specific compounds have been reported
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Structural studies of ribosome from an anaerobic Bacteroidetes human pathogen Porphyromonas gingivalis Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-30 Disha-Gajanan Hiregange, Sarit Samiya, Danuta Mizgalska, Efrat Ben-Zeev, Miriam Waghalter, Andre Rivalta, K Shanmugha Rajan, Yehuda Halfon, Elinor Breiner-Goldstein, Igor Kaczmarczyk, Aneta Sroka, Masato Taoka, Yuko Nobe, Toshiaki Isobe, Susanne Paukner, Ella Zimmerman, Anat Bashan, Jan Potempa, Ada Yonath
Porphyromonas gingivalis, an anaerobic pathogen in chronic periodontitis, belongs to the Bacteroidota phylum and is associated with various virulence factors. Its antibiotic-resistant strains and its propensity to form biofilms pose a challenge to effective treatment. To explore therapeutic avenues, we studied the high-resolution cryogenic electron microscope structures of ribosomes from the wild-type
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DNMT3A-dependent DNA methylation shapes the endothelial enhancer landscape Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-30 Stephanie Gehrs, Zuguang Gu, Joschka Hey, Dieter Weichenhan, Niklas Buckwalter, Moritz Jakab, Agnes Hotz-Wagenblatt, Kersten Breuer, Maria Llamazares Prada, Daniel Hübschmann, Katharina Schlereth, Christoph Plass, Hellmut Augustin
DNA methylation plays a fundamental role in regulating transcription during development and differentiation. However, its functional role in the regulation of endothelial cell (EC) transcription during state transition, meaning the switch from an angiogenic to a quiescent cell state, has not been systematically studied. Here, we report the longitudinal changes of the DNA methylome over the lifetime
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RNA-binding protein Ars2 mediates transcriptional silencing of telomeric repeats and transposable elements in the Drosophila germline Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-30 Valeriya Morgunova, Anastasiya A Kobelyatskaya, Maksim Erokhin, Olesya Sokolova, Tatyana V Sizova, Dmitry A Kwon, Alla Kalmykova
Telomeres ensure genome stability and the levels of telomeric RNA reflect the integrity of telomeric chromatin. The highly conserved RNA-binding protein Ars2 (Arsenite-resistance protein 2) plays an essential role in the RNA nuclear metabolism and negatively regulates the expression of telomeric transcripts in human cells and in Drosophila. We found that germline knockdown of Drosophila Ars2 does not
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Structural insight into the novel Thermus thermophilus SPOUT methyltransferase RlmR catalysing Um2552 formation in the 23S rRNA A-loop: a case of convergent evolution Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-30 Yousra Tanouti, Martine Roovers, Philippe Wolff, Antony Lechner, Dany Van Elder, André Feller, Romuald Soin, Cyril Gueydan, Véronique Kruys, Louis Droogmans, Geoffray Labar
The A-loop of the 23S ribosomal RNA is a critical region of the ribosome involved in stabilizing the CCA-end of A-site-bound transfer RNA. Within this loop, nucleotide U2552 is frequently 2′-O-methylated (Um2552) in various organisms belonging to the three domains of life. Until now, two enzymatic systems are known to modify this position, relying on either a Rossmann fold-like methyltransferase (RFM)
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Improved DNA binding to a type IV minor pilin increases natural transformation Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-30 Taylor J Ellison, Courtney K Ellison
Bacteria take up environmental DNA using dynamic appendages called type IV pili (T4P) to elicit horizontal gene transfer in a process called natural transformation. Natural transformation is widespread amongst bacteria yet the parameters that enhance or limit this process across species are poorly understood. We show that the most naturally transformable species known, Acinetobacter baylyi, owes this
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SRSF10 regulates oligodendrocyte differentiation during mouse central nervous system development by modulating pre-mRNA splicing Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-29 Yawei Mu, Zixuan Wei, Menghan Sun, Junjie Li, Yi Jiang, Hanyang Jiang, Ankangzhi Ma, Cuiqing Zhu, Xianhua Chen
We characterized the role and regulation mechanism of a pre-mRNA splicing factor, SRSF10, in the development of oligodendrocyte lineage cells (OLCs) and the myelination process during mouse central nervous system (CNS) development. We found that depletion of SRSF10 specifically in OLCs induces hypomyelination and a decrease in OLCs in the developing mouse CNS, whereas depletion of SRSF10 only in differentiated
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Preparation of topoisomers of short circular dsDNA with defined linking number by accurate topological control Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-28 Mengqin Liu, Ziyi Wang, Ran An, Angda Li, Xingguo Liang
Short DNA catenanes [circular double-stranded DNA (dsDNA)] have attracted considerable interest for constructing nanostructures and nanomachines, as well as understanding DNA topology. The study of topoisomers of a circular dsDNA with a definite linking number (Lk) is essential but very difficult for simplifying the complex problems about DNA topology. The topoisomers are difficult to prepare, especially
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Structural basis of G-quadruplex recognition by a camelid antibody fragment Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-28 Mojca Pevec, Tadej Medved, Matic Kovačič, Neža Žerjav, Jernej Imperl, Janez Plavec, Jurij Lah, Remy Loris, San Hadži
Apart from the iconic Watson–Crick duplex, DNA can fold into different noncanonical structures, of which the most studied are G-quadruplexes (G4s). Despite mounting structural and biophysical evidence, their existence in cells was controversial until their detection using G4-specific antibodies. However, it remains unknown how antibodies recognize G4s at the molecular level and why G4-specific antibodies
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3D genome organization shapes DNA damage susceptibility to platinum-based drugs Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-28 Ye Wang, Asli Yildirim, Lorenzo Boninsegna, Valentina Christian, Sung-Hae L Kang, Xianghong Jasmine Zhou, Frank Alber
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
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Ribosomal expansion segment contributes to translation fidelity via N-terminal processing of ribosomal proteins Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-28 Riku Nagai, Olivia L Milam, Tatsuya Niwa, William J Howell, Jacob A Best, Hideji Yoshida, Carver D Freeburg, John M Koomen, Kotaro Fujii
Eukaryotic ribosomes exhibit higher mRNA translation fidelity than prokaryotic ribosomes, partly due to eukaryote-specific ribosomal RNA (rRNA) insertions. Among these, expansion segment 27L (ES27L) on the 60S subunit enhances fidelity by anchoring methionine aminopeptidase (MetAP) at the nascent protein exit tunnel, accelerating co-translational N-terminal initiator methionine (iMet) processing. However
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SCIG: Machine learning uncovers cell identity genes in single cells by genetic sequence codes Nucleic Acids Res. (IF 16.6) Pub Date : 2025-05-28 Kulandaisamy Arulsamy, Bo Xia, Yang Yu, Hong Chen, William T Pu, Lili Zhang, Kaifu Chen
Deciphering cell identity genes is pivotal to understanding cell differentiation, development, and cell identity dysregulation involving diseases. Here, we introduce SCIG, a machine-learning method to uncover cell identity genes in single cells. In alignment with recent reports that cell identity genes (CIGs) are regulated with unique epigenetic signatures, we found CIGs exhibit distinctive genetic