Subject: Nucleic Acids Research Table of Contents for 27 January 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 2
 
27 January 2025
 
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NAR Breakthrough Article
 
 
 
 
RNA binding by Periphilin plays an essential role in initiating silencing by the HUSH complex 
 
Stuart Bloor, Niek Wit, Paul J Lehner
 
 
 
A comprehensive analysis framework for evaluating commercial single-cell RNA sequencing technologies 
 
Marco De Simone, Jonathan Hoover, Julia Lau, Hayley M Bennett, Bing Wu ...
 
 
 
Critical Reviews and Perspectives
 
 
 
 
Kinetoplast DNA: a polymer physicist's topological Olympic dream 
 
Davide Michieletto
 
 
 
Defining gene ends: RNA polymerase II CTD threonine 4 phosphorylation marks transcription termination regions genome-wide 
 
Magda Kopczy"ska, Upasana Saha, Anastasiia Romanenko, Takayuki Nojima, Michał R Gdula ...
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
Engineered initiator tRNAs can effectively start translation at non-AUG start codons and diversify N-terminal amino acids for mRNA Display 
 
Christina Helmling, Alix I Chan, Christian N Cunningham
 
 
 
 
 
Computational Biology
 
 
 
 
BASAL: a universal mapping algorithm for nucleotide base-conversion sequencing 
 
Moping Xu, Xiaoyang Liu, Miao Wang, Tingting Luo, Yawei Gao ...
 
 
 
Generative design-enabled exploration of wireframe DNA origami nanostructures  
 
Anthony J Vetturini, Jonathan Cagan, Rebecca E Taylor
 
 
 
Data Resources and Analyses
 
 
 
 
Mapping the spatial atlas of the human bone tissue integrating spatial and single-cell transcriptomics 
 
Weiqiang Lin, Yisu Li, Chuan Qiu, Binghao Zou, Yun Gong ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
Distinct structural and functional heterochromatin partitioning of lamin B1 and lamin B2 revealed using genome-wide nicking enzyme epitope targeted DNA sequencing 
 
Sagnik Sen, Pierre-Olivier Estève, Karthikeyan Raman, Julie Beaulieu, Hang Gyeong Chin ...
 
 
 
Modular organization of enhancer network provides transcriptional robustness in mammalian development 
 
Hongli Lin, Xinyun Ye, Wenyan Chen, Danni Hong, Lifang Liu ...
 
 
 
 
Novel role of zinc-finger protein 518 in heterochromatin formation on alpha -satellite DNA 
 
Shinya Ohta, Jun-Ichirou Ohzeki, Nobuko Sato, Hideki Tanizawa, Claire Yik-Lok Chung ...
 
 
 
Downregulation of MLF1 safeguards cardiomyocytes against senescence-associated chromatin opening 
 
Jian Lv, Qin Chen, Junmei Wang, Ningning Guo, Yu Fang ...
 
 
 
Long G4-rich enhancers target promoters via a G4 DNA-based mechanism  
 
Jeffrey D DeMeis, Justin T Roberts, Haley A Delcher, Noel L Godang, Alexander B Coley ...
 
 
 
Conformational switching of Arp5 subunit regulates INO80 chromatin remodeling  
 
Shagun Shukla, Somnath Paul, Jeison Garcia, Yuan Zhong, Sara Sanz Juste ...
 
 
 
Convergent pairs of highly transcribed genes restrict chromatin looping in Dictyostelium discoideum  
 
Irina V Zhegalova, Sergey V Ulianov, Aleksandra A Galitsyna, Ilya A Pletenev, Olga V Tsoy ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
The pathway to resolve dimeric forms distinguishes plasmids from megaplasmids in Enterobacteriaceae 
 
Florian Fournes, Manuel Campos, Jean Cury, Caroline Schiavon, Carine Pagès ...
 
 
 
Evidence for intrinsic DNA dynamics and deformability in damage sensing by the Rad4/XPC nucleotide excision repair complex 
 
Saroj Baral, Sagnik Chakraborty, Peter J Steinbach, Debamita Paul, Jung-Hyun Min ...
 
 
 
Extensive homologous recombination safeguards oocyte genome integrity in mammals 
 
Huiwen Cao, Cheng Qiu, Anxuan Fang, Jianzhou Shang, Wei Xu ...
 
 
 
Negative DNA supercoiling enhances DARS2 binding of DNA-bending protein IHF in the activation of Fis-dependent ATP-DnaA production 
 
Kazutoshi Kasho, Kenya Miyoshi, Mizuki Yoshida, Ryuji Sakai, Sho Nakagawa ...
 
 
 
TDP1 splice-site mutation causes HAP1 cell hypersensitivity to topoisomerase I inhibition 
 
Chen Gang Goh, Aldo S Bader, Tuan-Anh Tran, Rimma Belotserkovskaya, Giuseppina D'Alessandro ...
 
 
 
Degradation and stable maintenance of adeno-associated virus inverted terminal repeats in E. coli  
 
Marco T Radukic, Dinh To Le, Timo Krassuski, Philipp Borchert, David R F Leach ...
 
 
 
Genome-wide mapping of spontaneous DNA replication error-hotspots using mismatch repair proteins in rapidly proliferating Escherichia coli  
 
Flavia C Hasenauer, Hugo C Barreto, Chantal Lotton, Ivan Matic
 
 
 
Novel BRCA1'PLK1'CIP2A axis orchestrates homologous recombination-mediated DNA repair to maintain chromosome integrity during oocyte meiosis 
 
Crystal Lee, Jeong Su Oh
 
 
 
Genomics
 
 
 
 
Single-nucleotide-resolution genomic maps of O6 -methylguanine from the glioblastoma drug temozolomide 
 
Jasmina Kubitschek, Vakil Takhaveev, Cécile Mingard, Martha I Rochlitz, Patricia B Reinert ...
 
 
 
Comprehensive genome annotation of the model ciliate Tetrahymena thermophila by in-depth epigenetic and transcriptomic profiling 
 
Fei Ye, Xiao Chen, Yuan Li, Aili Ju, Yalan Sheng ...
 
 
 
ZNF143 binds DNA and stimulates transcription initiation to activate and repress direct target genes 
 
Jinhong Dong, Kizhakke Mattada Sathyan, Thomas G Scott, Rudradeep Mukherjee, Michael J Guertin
 
 
 
Enhanced detection and genotyping of disease-associated tandem repeats using HMMSTR and targeted long-read sequencing 
 
Kinsey Van Deynze, Camille Mumm, Connor J Maltby, Jessica A Switzenberg, Peter K Todd ...
 
 
 
Molecular and Structural Biology
 
 
 
 
Nonlinear regulatory dynamics of bacterial restriction-modification systems modulates horizontal gene transfer susceptibility 
 
Magdalena Djordjevic, Lidija Zivkovic, Hong-Yu Ou, Marko Djordjevic
 
 
 
The iMab antibody selectively binds to intramolecular and intermolecular i-motif structures 
 
Emanuela Ruggiero, Maja Marušič, Irene Zanin, Cristian David Peña Martinez, Daniel Christ ...
 
 
 
Transcription factors induce differential splicing of duplicated ribosomal protein genes during meiosis 
 
Cyrielle Petibon, Mathieu Catala, Danna Morales, Shanker Shyam Panchapakesan, Peter J Unrau ...
 
 
 
Embedding a ribonuclease in the spore crust couples gene expression to spore development in Bacillus subtilis  
 
Alexandre D'Halluin, Laetitia Gilet, Armand Lablaine, Olivier Pellegrini, Mónica Serrano ...
 
 
 
An integrated approach for the accurate detection of HERV-K HML-2 transcription and protein synthesis 
 
Charles Gleason, Sandra N Terry, Matthew M Hernandez, Samson Jacob, David Fenyo ...
 
 
 
DNA binding and transposition activity of the Sleeping Beauty transposase: role of structural stability of the primary DNA-binding domain 
 
Venkatesh V Ranjan, Gage O Leighton, Chenbo Yan, Maria Arango, Janna Lustig ...
 
 
 
The binding of RbgA to a critical 50S assembly intermediate facilitates YphC function in bacterial ribosomal assembly 
 
Dominic Arpin, Armando Palacios, Kaustuv Basu, Joaquin Ortega
 
 
 
The phage protein paratox is a multifunctional metabolic regulator of Streptococcus  
 
Tasneem Hassan Muna, Nicole R Rutbeek, Julia Horne, Ying W Lao, Oleg V Krokhin ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
A mobile genetic element-derived primase-polymerase harbors multiple activities implicated in DNA replication and repair 
 
Pan Fu, Yuwei Wang, Yanqiu Liu, Zhenhao Han, Zhangzhong Peng ...
 
 
 
Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes 
 
Kenny Jungfer, Štefan Moravčík, Carmela Garcia-Doval, Anna Knörlein, Jonathan Hall ...
 
 
 
Splice-at-will' Cas12a crRNA engineering enabled direct quantification of ultrashort RNAs 
 
Xinrui Fei, Chao Lei, Wei Ren, Chenghui Liu
 
 
 
The SARS-CoV-2 nucleocapsid protein interferes with the full enzymatic activation of UPF1 and its interaction with UPF2 
 
Veronica Nuccetelli, Makram Mghezzi-Habellah, Séverine Deymier, Armelle Roisin, Francine Gérard-Baraggia ...
 
 
 
CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation  
 
Katarzyna M Soczek, Joshua C Cofsky, Owen T Tuck, Honglue Shi, Jennifer A Doudna
 
 
 
Lig3-dependent rescue of mouse viability and DNA double-strand break repair by catalytically inactive Lig4 
 
David Medina-Suárez, Li Han, Sandra O'Reilly, Jiali Liu, Chao Wei ...
 
 
 
Protein-free catalysis of DNA hydrolysis and self-integration by a ribozyme  
 
Deni Szokoli, Hannes Mutschler
 
 
 
Alkylated DNA repair by a novel HhH-GPD family protein from Crenarchaea  
 
Likui Zhang, Tian Gao, Zheng Li, Cai Chen, Donghao Jiang ...
 
 
 
RNA and RNA-protein complexes
 
 
 
 
Novel archaeal ribosome dimerization factor facilitating unique 30S'30S dimerization 
 
Ahmed H Hassan, Matyas Pinkas, Chiaki Yaeshima, Sonoko Ishino, Toshio Uchiumi ...
 
 
 
Cryo-EM structure of human TUT1:U6 snRNA complex  
 
Seisuke Yamashita, Kozo Tomita
 
 
 
KRBP72 facilitates ATPase-dependent editing progression through a structural roadblock in mitochondrial A6 mRNA 
 
Ashutosh P Dubey, Brianna L Tylec, Soon Yi, Frank A Tedeschi, Joseph T Smith ...
 
 
 
Spatial regulation of NSUN2-mediated tRNA m5 C installation in cognitive function 
 
Yulia Gonskikh, Christian Tirrito, Praneeth Bommisetti, Maria Saraí Mendoza-Figueroa, Julian Stoute ...
 
 
 
Trypanosoma cruzi eIF4E3- and eIF4E4-containing complexes bind different mRNAs and may sequester inactive mRNAs during nutritional stress 
 
Bernardo Papini Gabiatti, Eden Ribeiro Freire, Jimena Ferreira da Costa, Mariana Galvão Ferrarini, Tatiana Reichert Assunção de Matos ...
 
 
 
Tissue-specific modulation of CRISPR activity by miRNA-sensing guide RNAs  
 
Antonio Garcia-Guerra, Chaitra Sathyaprakash, Olivier G de Jong, Wooi F Lim, Pieter Vader ...
 
 
 
Structural Biology
 
 
 
 
Structural plasticity of the coiled'coil interactions in human SFPQ 
 
Heidar J Koning, Jia Y Lai, Andrew C Marshall, Elke Stroeher, Gavin Monahan ...
 
 
 
Interaction of N-methylmesoporphyrin IX with a hybrid left-/right-handed G-quadruplex motif from the promoter of the SLC2A1 gene 
 
Paul Seth, Eric Xing, Andrew D Hendrickson, Kevin Li, Robert Monsen ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
A cross-species inducible system for enhanced protein expression and multiplexed metabolic pathway fine-tuning in bacteria 
 
Yang Li, Yaokang Wu, Xianhao Xu, Yanfeng Liu, Jianghua Li ...
 
 
 
Synthetic rational design of live-attenuated Zika viruses based on a computational model 
 
Modi Roopin, Zohar Zafrir, Bunpote Siridechadilok, Amporn Suphatrakul, Justin Julander ...
 
 
 
A trigger-inducible split-Csy4 architecture for programmable RNA modulation  
 
Lihang Zhang, Xinyuan Qiu, Yuting Zhou, Zhengyang Luo, Lingyun Zhu ...
 
 
 
High throughput variant libraries and machine learning yield design rules for retron gene editors 
 
Kate D Crawford, Asim G Khan, Santiago C Lopez, Hani Goodarzi, Seth L Shipman
 
 
 
Precision genome editing using combinatorial viral vector delivery of CRISPR-Cas9 nucleases and donor DNA constructs 
 
Zhen Li, Xiaoling Wang, Josephine M Janssen, Jin Liu, Francesca Tasca ...
 
 
 
A tunable and reversible thermo-inducible bio-switch for streptomycetes  
 
Lanxin Lv, Shuo Liu, Yudie Fu, Yuxin Zhang, Meiyan Wang ...
 
 
 
Methods
 
 
 
 
GDBr: genomic signature interpretation tool for DNA double-strand break repair mechanisms 
 
Hyunwoo Ryu, Hyunho Han, Chuna Kim, Jun Kim
 
 
 
inDrops-2: a flexible, versatile and cost-efficient droplet microfluidic approach for high-throughput scRNA-seq of fresh and preserved clinical samples 
 
Simonas Juzenas, Karolis Goda, Vaidotas Kiseliovas, Justina Zvirblyte, Alvaro Quintinal-Villalonga ...
 
 
 
GENA-LM: a family of open-source foundational DNA language models for long sequences 
 
Veniamin Fishman, Yuri Kuratov, Aleksei Shmelev, Maxim Petrov, Dmitry Penzar ...
 
 
 
Cre-Lox miRNA-delivery technology optimized for inducible microRNA and gene-silencing studies in zebrafish 
 
Fangfei Guo, Alisha Tromp, Haitao Wang, Thomas E Hall, Jean Giacomotto
 
 
 
DesiRNA: structure-based design of RNA sequences with a replica exchange Monte Carlo approach 
 
Tomasz K Wirecki, Grzegorz Lach, Nagendar Goud Badepally, S Naeim Moafinejad, Farhang Jaryani ...
 
 
 
Functional RNA mining using random high-throughput screening  
 
Li-Hua Liu, Jinde Chen, Shijing Lai, Xuemei Zhao, Min Yang ...
 
 
 
Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems 
 
Sean R Johnson, Peter R Weigele, Alexey Fomenkov, Andrew Ge, Anna Vincze ...
 
 
 
Imaging of endogenous RNA in live cells using sequence-activated fluorescent RNA probes 
 
Haifeng Zheng, Xiyu Liu, Luhui Liu, Jiarui Hu, Xianjun Chen
 
 
 
A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei  
 
Thorey K Jonsdottir, Martina S Paoletta, Takahiro Ishizaki, Sophia Hernandez, Maria Ivanova ...
 
 
 
edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets 
 
Yunshun Chen, Lizhong Chen, Aaron T L Lun, Pedro L Baldoni, Gordon K Smyth
 
 
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