Subject: Nucleic Acids Research Table of Contents for 10 February 2025 Oxford Academic
 
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20 Years of Open Access
 
In 2005 Nucleic Acids Research (NAR) transitioned from a subscription-based publishing model to an open access model. Now, 20 years later, NAR proudly stands as a leading journal in the field of biological sciences, providing barrier-free access to groundbreaking research.

To celebrate this milestone, we have created collection featuring the most cited paper (from standard article types) from each year since 2005. This collection showcases the research excellence that NAR fosters and demonstrates the impact of open access publishing.

Browse the papers
 
 
 
Nucleic Acids Research  
Volume 53 Issue 3
 
10 February 2025
 
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NAR Breakthrough Article
 
 
 
 
Genome-wide identification of bacterial genes contributing to nucleus-forming jumbo phage infection 
 
Kate R Harding, Lucia M Malone, Natalie A P Kyte, Simon A Jackson, Leah M Smith ...
 
 
 
Critical Reviews and Perspectives
 
 
 
 
Diversity and evolution of viroids and viroid-like agents with circular RNA genomes revealed by metatranscriptome mining 
 
Eugene V Koonin, Benjamin D Lee
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
Proximity-activated guide RNA of CRISPR'Cas12a for programmable diagnostic detection and gene regulation 
 
Zhian Hu, Shen Ling, Jialin Duan, Zixiao Yu, Yanfei Che ...
 
 
 
RNA G-quadruplex structure-based PROTACs for targeted DHX36 protein degradation and gene activity modulation in mammalian cells 
 
Kun Zhang, Qichang Nie, Maolin Li, Xiaona Chen, Liting Zhong ...
 
 
 
Direct repeat region 3² end modifications regulate Cas12a activity and expand its applications 
 
Wei Zhang, Yinyin Zhong, Jiaqi Wang, Guangrong Zou, Qiaozhen Chen ...
 
 
 
 
 
Computational Biology
 
 
 
 
Improving the generalization of protein expression models with mechanistic sequence information 
 
Yuxin Shen, Grzegorz Kudla, Diego A Oyarzún
 
 
 
Telomemore enables single-cell analysis of cell cycle and chromatin condensation 
 
Iryna Yakovenko, Ionut Sebastian Mihai, Martin Selinger, William Rosenbaum, Andy Dernstedt ...
 
 
 
Data Resources and Analyses
 
 
 
 
G-quadruplex structures in 16S rRNA regions correlate with thermal adaptation in prokaryotes 
 
Bo Lyu, Kangkang Niu, Deborah Anderson, Qili Feng, Qisheng Song
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
c-JUN: a chromatin repressor that limits mesoderm differentiation in human pluripotent stem cells 
 
Ran Zhang, Guihuan Li, Qi Zhang, Zhenhua Wang, Dan Xiang ...
 
 
 
Genomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at super-enhancers 
 
Shengyuan Wang, Zhenjia Wang, Chongzhi Zang
 
 
 
 
Fam170a deficiency causes male infertility by impairing histone-to-protamine exchange during mouse spermiogenesis 
 
Jinmei Cheng, Yimin Gu, Yueming Wang, Junjie Xun, Guishuan Wang ...
 
 
 
Methyl-dependent auto-regulation of the DNA N6-adenine methyltransferase AMT1 in the unicellular eukaryote Tetrahymena thermophila  
 
Lili Duan, Haicheng Li, Aili Ju, Zhe Zhang, Junhua Niu ...
 
 
 
The ortholog of human DNAJC9 promotes histone H3'H4 degradation and is counteracted by Asf1 in fission yeast 
 
Yan Ding, Jun Li, He-Li Jiang, Fang Suo, Guang-Can Shao ...
 
 
 
A high-resolution view of RNA endonuclease cleavage in Bacillus subtilis  
 
James C Taggart, Kathryn Julia Dierksheide, Hannah J LeBlanc, Jean-Benoît Lalanne, Sylvain Durand ...
 
 
 
SLAM-seq reveals independent contributions of RNA processing and stability to gene expression in African trypanosomes 
 
Vanessa Luzak, Esteban Osses, Anna Danese, Christoff Odendaal, Raúl O Cosentino ...
 
 
 
tRNA hypomodification facilitates 5-fluorocytosine resistance via cross-pathway control system activation in Aspergillus fumigatus  
 
Alexander Bruch, Valentina Lazarova, Maximilian Berg, Thomas Krüger, Sascha Schäuble ...
 
 
 
Hypoxia increases methylated histones to prevent histone clipping and heterochromatin redistribution during Raf -induced senescence 
 
Soojeong Chang, Ramhee Moon, Dowoon Nam, Sang-Won Lee, Insoo Yoon ...
 
 
 
Chromatin remodeler CHD4 establishes chromatin states required for ovarian reserve formation, maintenance and male germ cell survival 
 
Yasuhisa Munakata, Mengwen Hu, Yuka Kitamura, Raissa G Dani, Adam L Bynder ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
Transcription near arrested DNA replication forks triggers ribosomal DNA copy number changes 
 
Mariko Sasaki, Takehiko Kobayashi
 
 
 
Dual DNA replication modes: varying fork speeds and initiation rates within the spatial replication program in Xenopus  
 
Diletta Ciardo, Olivier Haccard, Francesco de Carli, Olivier Hyrien, Arach Goldar ...
 
 
 
The interplay of the translocase activity and protein recruitment function of PICH in ultrafine anaphase bridge resolution and genomic stability 
 
Nannan Kong, Kun Chen, Primrose Chanboonyasitt, Huadong Jiang, Ka Yan Wong ...
 
 
 
Mlh1-Pms1 ATPase activity is regulated distinctly by self-generated nicks and strand discrimination signals in mismatch repair 
 
Jonathan M Piscitelli, Scott J Witte, Yasmine S Sakinejad, Carol M Manhart
 
 
 
DNA polymerase zeta can efficiently replicate structures formed by AT/TA repeat sequences and prevent their deletion 
 
Mili Das, Suzanne E Hile, Jennifer Brewster, Jan Leendert Boer, Rachel Bezalel-Buch ...
 
 
 
The ATPase activity of yeast chromosome axis protein Hop1 affects the frequency of meiotic crossovers 
 
Kshitiza M Dhyani, Suman Dash, Sameer Joshi, Aditi Garg, Debnath Pal ...
 
 
 
Genomics
 
 
 
 
Hybrid exons evolved by coupling transcription initiation and splicing at the nucleotide level 
 
Steven T Mick, Christine L Carroll, Maritere Uriostegui-Arcos, Ana Fiszbein
 
 
 
Molecular and Structural Biology
 
 
 
 
Inhibition of HMGA2 binding to AT-rich DNA by its negatively charged C-terminus 
 
Linjia Su, Zifang Deng, Miguel Santos-Fernandez, Kevin Jeanne Dit Fouque, Prem P Chapagain ...
 
 
 
Selection of initiator tRNA and start codon by mammalian mitochondrial initiation factor 3 in leaderless mRNA translation 
 
Muhoon Lee, Taisei Wakigawa, Qimin Jia, Chang Liu, Ruiyuan Huang ...
 
 
 
Influenza A virus NS2 protein acts on vRNA-resident polymerase to drive the transcription to replication switch 
 
Lei Zhang, Qiuxian Yang, Yuekun Shao, Shenyang Ding, Jiamei Guo ...
 
 
 
Early events in G-quadruplex folding captured by time-resolved small-angle X-ray scattering 
 
Robert C Monsen, T Michael Sabo, Robert Gray, Jesse B Hopkins, Jonathan B Chaires
 
 
 
Influenza a virus antiparallel helical nucleocapsid-like pseudo-atomic structure 
 
Florian Chenavier, Eleftherios Zarkadas, Lily-Lorette Freslon, Alice J Stelfox, Guy Schoehn ...
 
 
 
Mutagenesis studies suggest a mechanism for influenza polymerase stalling during polyadenylation 
 
Minke Li, Yixi Wu, Huanhuan Li, Wenjun Song, Zhenxing Chen ...
 
 
 
Genome-wide phenotypic profiling of transcription factors and identification of novel targets to control the virulence of Vibrio vulnificus  
 
Dayoung Sung, Garam Choi, Minji Ahn, Hokyung Byun, Tae Young Kim ...
 
 
 
Site-specific free energy surface parameters from single-molecule fluorescence measurements of exciton-coupled (iCy3)2 dimer probes positioned at DNA replication fork junctions 
 
Jack Maurer, Claire S Albrecht, Peter H von Hippel, Andrew H Marcus
 
 
 
A gate-clamp mechanism for ssDNA translocation by DdmD in Vibrio cholerae plasmid defense 
 
Ruoyu Li, Yusong Liu, Haishan Gao, Zhonghui Lin
 
 
 
Molecular Biology
 
 
 
 
AAV vector transduction restriction and attenuated toxicity in hESCs via a rationally designed inverted terminal repeat 
 
Liujiang Song, Tomoko Hasegawa, Nolan J Brown, Jacquelyn J Bower, Richard J Samulski ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
A novel ADP-directed chaperone function facilitates the ATP-driven motor activity of SARS-CoV helicase 
 
Jeongmin Yu, Hyeryeon Im, HyeokJin Cho, Yongmoon Jeon, Jong-Bong Lee ...
 
 
 
Identification of an enzyme with strong single-stranded DNA ligation activity and its application for sequencing 
 
Fumihito Miura, Yukiko Shibata, Miki Miura, Kazune Inatomi, Yutaka Suzuki ...
 
 
 
Local structural dynamics of Rad51 protomers revealed by cryo-electron microscopy of Rad51-ssDNA filaments 
 
Jie Liu, Steven K Gore, Wolf-Dietrich Heyer
 
 
 
The membrane-targeting-sequence motif is required for exhibition of recessive resurrection in Escherichia coli RNase E 
 
Papri Basak, Manjula Ekka, Apuratha Pandiyan, Smriti Tandon, Jayaraman Gowrishankar
 
 
 
DNA target binding-induced pre-crRNA processing in type II and V CRISPR-Cas systems 
 
Jiyun Chen, Xiaofeng Lin, Wenwen Xiang, Ying Chen, Yueming Zhao ...
 
 
 
Neutrophil extracellular traps have active DNAzymes that promote bactericidal activity 
 
Ti-Hsuan Ku, Nikhil Ram-Mohan, Elizabeth J Zudock, Ryuichiro Abe, Samuel Yang
 
 
 
Large serine integrases utilise scavenged phage proteins as directionality cofactors 
 
Abdulrazak Alsaleh, Alexandria Holland, Heewhan Shin, Tania Pena Reyes, Aron Baksh ...
 
 
 
RNA and RNA-protein complexes
 
 
 
 
Transcriptome-scale analysis uncovers conserved residues in the hydrophobic core of the bacterial RNA chaperone Hfq required for small regulatory RNA stability 
 
Josh McQuail, Miroslav Krepl, Kai Katsuya-Gaviria, Aline Tabib-Salazar, Lynn Burchell ...
 
 
 
WBSCR16 is essential for mitochondrial 16S rRNA processing in mammals  
 
Shengjie Zhang, Zi Dong, Yang Feng, Wei Guo, Chen Zhang ...
 
 
 
The short conserved region-2 of LARP4 interacts with ribosome-associated RACK1 and promotes translation 
 
Amitabh Ranjan, Sandy Mattijssen, Nithin Charlly, Isabel Cruz Gallardo, Leah F Pitman ...
 
 
 
Antagonistic roles by the conserved nuclear poly(A)-binding proteins PABPN1 and ZC3H14 in nuclear RNA surveillance 
 
Mélodie Latour, Lauren Kwiatek, Anne-Marie Landry-Voyer, François Bachand
 
 
 
R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning 
 
Manuel Brenes-Álvarez, Halie R Ropp, Dimitrios Papagiannidis, Clement M Potel, Frank Stein ...
 
 
 
RNA elements required for the high efficiency of West Nile virus-induced ribosomal frameshifting 
 
Nikolay A Aleksashin, Conner J Langeberg, Rohan R Shelke, Tianhao Yin, Jamie H D Cate
 
 
 
5² terminal nucleotide determines the immunogenicity of IVT RNAs  
 
Magdalena Wolczyk, Jacek Szymanski, Ivan Trus, Zara Naz, Tola Tame ...
 
 
 
Two temperature-responsive RNAs act in concert: the small RNA CyaR and the mRNA ompX  
 
David A Guanzon, Stephan Pienkoß, Vivian B Brandenburg, Jennifer Röder, Daniel Scheller ...
 
 
 
Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics 
 
Brianna Bibel, Tushar Raskar, Mary Couvillion, Muhoon Lee, Jordan I Kleinman ...
 
 
 
Structural Biology
 
 
 
 
Cryo-EM structure of AAV2 Rep68 bound to integration site AAVS1: insights into the mechanism of DNA melting 
 
Rahul Jaiswal, Brandon Braud, Karen C Hernandez-Ramirez, Vishaka Santosh, Alexander Washington ...
 
 
 
Structural and mechanistic insights into the activation of a short prokaryotic argonaute system from archaeon Sulfolobus islandicus  
 
Zhikang Dai, Yu Chen, Zeyuan Guan, Xueting Chen, Keyi Tan ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
An evolved, orthogonal ssDNA generator for targeted hypermutation of multiple genomic loci 
 
Weiran Chu, Rongzhen Tian, Yaxin Guo, Yaokang Wu, Fabian B H Rehm ...
 
 
 
Phage-mediated intercellular CRISPRi for biocomputation in bacterial consortia  
 
Abhinav Pujar, Amit Pathania, Corbin Hopper, Amir Pandi, Cristian Ruiz Calderón ...
 
 
 
Methods
 
 
 
 
ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens 
 
Joon Young Park, Minchang Jang, Eunna Choi, Sang-Mok Lee, Ina Bang ...
 
 
 
methylGrapher: genome-graph-based processing of DNA methylation data from whole genome bisulfite sequencing 
 
Wenjin Zhang, Juan F Macias-Velasco, Xiaoyu Zhuo, Edward A Belter, Jr, Chad Tomlinson ...
 
 
 
Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning 
 
Maria Chernigovskaya, Milena Pavlović, Chakravarthi Kanduri, Sofie Gielis, Philippe A Robert ...
 
 
 
Measuring XNA polymerase fidelity in a hydrogel particle format  
 
Esau L Medina, John C Chaput
 
 
 
mRNA-LM: full-length integrated SLM for mRNA analysis  
 
Sizhen Li, Shahriar Noroozizadeh, Saeed Moayedpour, Lorenzo Kogler-Anele, Zexin Xue ...
 
 
 
A general strategy for engineering GU base pairs to facilitate RNA crystallization 
 
Yangyi Ren, Xiaowei Lin, Wenjian Liao, Xuemei Peng, Jie Deng ...
 
 
 
A modular toolbox for the optogenetic deactivation of transcription  
 
Philipp Muench, Matteo Fiumara, Nicholas Southern, Davide Coda, Sabine Aschenbrenner ...
 
 
 
Machine learning-optimized targeted detection of alternative splicing  
 
Kevin Yang, Nathaniel Islas, San Jewell, Di Wu, Anupama Jha ...
 
 
 
zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters 
 
Rauf Salamzade, Patricia Q Tran, Cody Martin, Abigail L Manson, Michael S Gilmore ...
 
 
 
Corrections
 
 
 
 
Correction to ˜DNA target binding-induced pre-crRNA processing in type II and V CRISPR-Cas systems' 
 
 
 
 
Correction to ˜ECBD: European chemical biology database' 
 
 
 
 
Editor's Note
 
 
 
 
Editor's Note on ˜MicroRNA-296 is enriched in cancer cells and downregulates p21WAF1 mRNA expression via interaction with its 3² untranslated region' 
 
 
 
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