Subject: New issue: Nucleic Acids Research, Volume 53, Issue 13, 22 July 2025

Nucleic Acids Research

Volume 53, Issue 13, 22 July 2025

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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

NAR Breakthrough Article

Coupling tRNA^Gly gene redundancy with staphylococcal cell wall integrity, antibiotic susceptibility, and virulence potential

Adamantia Kouvela and others

Critical Reviews and Perspectives

The ribosomal RNA transcription landscapes of Plasmodium falciparum and related apicomplexan parasites

Gunnar Mair and others

The biological and evolutionary consequences of competition between DNA sequences that benefit the cell and DNA sequences that benefit themselves

Arnold J Bendich and Scott O Rogers

DBR1 orchestrates the fate of lariat RNA: debranching-dependent turnover and function

Qi Tang and others

The XNA alphabet

John C Chaput and others

ADARs: pleiotropy in function, versatility in application

Yifan Zhang and others

Chemical Biology and Nucleic Acid Chemistry

A trackable trinuclear platinum complex for breast cancer treatment

SinÃ©ad O'Carroll and others

Computational Biology

Targeted genome mining with GATOR-GC maps the evolutionary landscape of biosynthetic diversity

JosÃ© D D Cediel-Becerra and others

Predicting rare DNA conformations via dynamical graphical models: a case study of the Bâ†'A transition

Namindu De Silva and Alberto Perez

DeepNanoHi-C: deep learning enables accurate single-cell nanopore long-read data analysis and 3D genome interpretation

Wenjing Ma and others

Gene Regulation, Chromatin and Epigenetics

Set1 is a critical transcriptional regulator in response to external signals in Candida albicans

Jueun Kim and others

Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization

Gony Shanel and others

SAGA subunits Spt3 and Spt8 act directly and non-redundantly with TFIID in TBP recruitment in the Gcn4 transcriptome

Sakshi Singh and Alan G Hinnebusch

Molecular determinants for recognition of serotonylated chromatin

Laura Pulido-CortÃ©s and others

Characterization of the MgsR-dependent promoter structure in Bacillus subtilis'application of a novel pHIS plasmid-based screening system for promoter element analysis

Marco Harms and others

Nucleolar FRG2 lncRNAs inhibit rRNA transcription and cytoplasmic translation, linking FSHD to dysregulation of muscle-specific protein synthesis

Valentina Salsi and others

The Mgv1'Rlm1 axis orchestrates SAGA and SWI/SNF complexes at target promoters

Chaoyun Xu and others

Specificity in clustering of gene-specific transcription factors is encoded in the genome

Shivali Dongre and Nadine L Vastenhouw

Regulation of a phage defence island by RptR, a novel repressor that controls restriction'modification systems in diverse bacteria

YuGeng Zhang and others

Re-establishment of H3K9me2 eliminates the transcriptional inhibition of ST18 on meiotic genes and orchestrates female germ cell development

Bing-Wang Zhao and others

sRNA-mediated crosstalk between cell wall stress and galactose metabolism in Staphylococcus aureus

MaÃ«liss Germain and others

Histone H3 N-terminal recognition by the PHD finger of PHRF1 is required for proper DNA damage response

Kanishk Jain and others

Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs

Alyssa M Ekdahl and others

Genome Integrity, Repair and Replication

A cancer persistent DNA repair circuit driven by MDM2, MDM4 (MDMX), and mutant p53 for recruitment of MDC1 and 53BP1 on chromatin

Viola Ellison and others

BTG3-dependent VCP/p97 nuclear translocation is required for efficient repair of UV-induced DNA lesions

Jack Dalit Acedera and others

CDK-driven phosphorylation of TRAIP is essential for mitotic replisome disassembly and MiDAS

Divyasree Poovathumkadavil and others

Relaxed DNA substrate specificity of transposases involved in programmed genome rearrangement

Matt W G Walker and others

The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1

Md Bayejid Hosen and others

The dual ubiquitin binding mode of SPRTN secures rapid spatiotemporal proteolysis of DNA'protein crosslinks

Wei Song and others

A human high-fidelity DNA polymerase holoenzyme has a wide range of lesion bypass activities

Rachel L Dannenberg and others

Genomics

Telomeric repeat-containing RNA increases in aged human cells

Yu-Hung Hsieh and others

Horizontal acquisition of the Type I restriction'modification system enhances bacterial pathogenicity by mediating methylation of transcription factor-encoding genes

Jiayue Ma and others

Comparative mitochondrial genome and transcriptome analyses reveal strain-specific features of RNA editing in Trypanosoma brucei

Xiaojing Zhao and others

Molecular and Structural Biology

A molecular switch at the yeast mitoribosomal tunnel exit controls cytochrome b synthesis

Andreas CarlstrÃ¶m and others

Elucidating the role of mycobacteriophage D29-encoded Gp36 in DNA binding and phage gene expression regulation

Swathy Sasidharan Pillai and Vikas Jain

Antitoxin control of optimal transcriptional repression in the atypical HigB'HigA toxin'antitoxin system from Proteus vulgaris

Ian J Pavelich and others

Sequence, structure, and affinity of miR-34a binding sites determine repression efficacy

Lara Sweetapple and others

Nucleic Acid Enzymes

SAM-AMP lyases in type III CRISPR defence

Haotian Chi and others

A transfer RNA methyltransferase with an unusual domain composition catalyzes 2²-O-methylation at position 6 in tRNA

Teppei Matsuda and others

Structural and mechanistic insights into the sequential dsDNA cleavage by SpCas12f1

Julene Madariaga-Marcos and others

Nucleic Acid Therapeutics

Dissecting the epigenetic regulation of the fetal hemoglobin genes to unravel a novel therapeutic approach for beta -hemoglobinopathies

Simone Amistadi and others

ACE-tRNAs are a platform technology for suppressing nonsense mutations that cause cystic fibrosis

Wooree Ko and others

Splice-modulating antisense oligonucleotides targeting a pathogenic intronic variant in adult polyglucosan body disease correct mis-splicing and restore enzyme activity in patient cells

Ria Thomas and others

RNA and RNA-protein complexes

Distant ribose 2²-O-methylation of 23S rRNA helix 69 pre-orders the capreomycin drug binding pocket at the ribosome subunit interface

Suparno Nandi and others

Global analysis of the Hfq-mediated RNA interactome discovers a MicA homolog that affects the cytotoxicity, biofilm formation, and resistance to complement of Bordetella pertussis

Dilip Kumar and others

A tRNA gene potential to activate interferon signaling involves selective termination and is suppressible by La protein/SSB

Alan C Kessler and others

FASTKD5 processes mitochondrial pre-mRNAs at noncanonical cleavage sites

Hana Antonicka and others

Key RNA-binding domains in the La protein establish tRNA modification levels in Trypanosoma brucei

Lankani Gunaratne and others

A-to-I mRNA editing recodes hundreds of genes in dozens of species and produces endogenous protein isoforms in bacteria

Eyal Elias and others

An endoribonuclease of the YicC-like family delays sporulation via sRNA degradation in Clostridioides difficile

Diogo Martins and others

Directed evolution expands CRISPR'Cas12a genome-editing capacity

Enbo Ma and others

Synthetic Biology and Bioengineering

Expanding genetic engineering capabilities in Vibrio natriegens with the Vnat Collection

Anna Faber and others

Methods

Tunable fluorogenic DNA probes drive fast and high-resolution single-molecule fluorescence imaging

Mirjam KÃ¼mmerlin and others

DiCE: differential centrality-ensemble analysis based on gene expression profiles and protein'protein interaction network

Elnaz Pashaei and others

Comprehensive analysis of mutational processes across 20 000 adult and pediatric tumors

Matteo Villa and others

Enhancing sequence alignment of adaptive immune receptors through multi-task deep learning

Thomas Konstantinovsky and others

Design of mismatch closure for enhanced specificity in DNA strand displacement reactions

Hongyan Yu and others

Corrections

Correction to ˜BASAL: a universal mapping algorithm for nucleotide base-conversion sequencing'

Correction to ˜PAM-free hairpin target binding activates trans-cleavage activity of Cas12a'

Correction to ˜In vitro programmable DNA cleavage by a eukaryotic Argonaute'

Correction to ˜A method for in-depth analysis of circular DNA virus populations by unambiguously profiling the low abundant virus variants and partial genomic components'

20th Open Access Anniversary

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