Subject: New issue: Nucleic Acids Research, Volume 53, Issue 7, 24 April 2025

Nucleic Acids Research

Volume 53, Issue 7, 24 April 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

Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network

Thomas Stuart Wilson and others

Critical Reviews and Perspectives

Decoding the complex journeys of RNAs along neurons

Jenna L Wingfield and Sathyanarayanan V Puthanveettil

Chemical Biology and Nucleic Acid Chemistry

Tailoring and reversing m⁶A editing with sequential RNA bioorthogonal chemistry

Xingyu Liu and others

Naphthalene diimide-naphthalimide dyads promote telomere damage by selectively targeting multimeric G-quadruplexes

Valentina Pirota and others

Investigating the interplay between RNA structural dynamics and RNA chemical probing experiments

Ethan B Arnold and others

Computational Biology

Analysis of RNA translation with a deep learning architecture provides new insight into translation control

Xiaojuan Fan and others

Benchmarking computational methods for detecting spatial domains and domain-specific spatially variable genes from spatial transcriptomics data

Liping Kang and others

Data Resources and Analyses

High-throughput screen of 100 000 small molecules in C9ORF72 ALS neurons identifies spliceosome modulators that mobilize G4C2 repeat RNA into nuclear export and repeat associated non-canonical translation

Maartje J Luteijn and others

Gene Regulation, Chromatin and Epigenetics

A specific pluripotency-associated eRNA controls Nanog locus by shaping the epigenetic landscape and stabilizing enhancer'promoter interaction

Mariella Cuomo and others

Nuclear actin-dependent Meg3 expression suppresses metabolic genes by affecting the chromatin architecture at sites of elevated H3K27 acetylation levels

Nadine Hosny El Said and others

The ZBTB24-CDCA7-HELLS axis suppresses the totipotent 2C-like reprogramming by maintaining Dux methylation and repression

Dan Guo and others

Maternal histone mRNAs are uniquely processed through polyadenylation in a Stem-Loop Binding Protein (SLBP) dependent manner

Juan PÃ©rez-RoldÃ¡n and others

Transcriptional induction by ecdysone in Drosophila salivary glands involves an increase in chromatin accessibility and acetylation

Aleksandra A Evdokimova and others

Single-stranded DNA drives Ïƒ subunit loading onto mycobacterial RNA polymerase to unlock initiation-competent conformations

Rishi Kishore Vishwakarma and others

Nutrient starvation-induced Hda1C rewiring: coordinated regulation of transcription and translation

Min Kyung Lee and others

Genome Integrity, Repair and Replication

Light-controlled Spo11-less meiotic DNA breaks by MagTAQing lead to chromosomal aberrations

Hideyuki Yone and others

The PIN1'p38'CtIP signalling axis protects stalled replication forks from deleterious degradation

Francesca Vivalda and others

Oxidative stress at telomeres triggers internal DNA loops, TRF1 dissociation, and TRF2-dependent R-loops

Trang Thu Nguyen and others

Poly-(ADP-ribose) serves as a scaffold for the methyltransferase METTL3/14 complex in the DNA damage response

Claudia Gonzalez-Leal and others

The yeast CST and Polalpha /primase complexes act in concert to ensure proper telomere maintenance and protection

Kimberly Calugaru and others

The linker region of a development-specific DNA polymerase X ensures efficient repair of programmed DNA double-strand breaks in Paramecium tetraurelia

Baptiste Verron and others

UV induces codirectional replication'transcription conflicts and an alternative DnaA-dependent replication origin in the rnhAB mutants of Escherichiacoli

Elena A Kouzminova and others

Genomics

Non-canonical DNA in human and other ape telomere-to-telomere genomes

LinnÃ©a Smeds and others

High-resolution mapping of sigma factor DNA-binding sequences using artificial promoters, RNA aptamers, and deep sequencing

Essa Ahsan Khan and others

Molecular and Structural Biology

Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits

Federica Fiorentino and others

Impacts of sequence and structure on pyrrolocytosine fluorescence in RNA

Taylor L Coulson and Julia R Widom

Activation, incompatibility, and displacement of FIB replicons in E. coli

Georgina S Lloyd and others

A two-step regulatory mechanism dynamically controls histone H3 acetylation by SAGA complex at growth-related promoters

Sevil Zencir and others

Autophagy induction enhances homologous recombination-associated CRISPR'Cas9 gene editing

Hye Jin Nam and others

Proteome-wide microarray-based screening of PAR-binding proteins

Bong Gu Kang and others

Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants

Qiong Liu and others

Nucleic Acid Enzymes

CRISPR RNA binding drives structural ordering that primes Cas7-11 for target cleavage

Calvin P Lin and others

Cryo-EM structures of DNA-free and DNA-bound BsaXI: architecture of a Type IIB restriction'modification enzyme

Betty W Shen and others

Molecular basis for RNA discrimination by human DNA ligase 1

Percy P Tumbale and others

Nucleic Acid Therapeutics

Conjugation to a transferrin receptor 1-binding Bicycle peptide enhances ASO and siRNA potency in skeletal and cardiac muscles

Michael E Ã˜stergaard and others

RNA and RNA-protein complexes

Nuclear AGO2 supports influenza A virus replication through type-I interferon regulation

Hsiang-Chi Huang and others

Chromatin-associated alpha -satellite RNA maintains chromosome stability by reestablishing SAF-A in the mitotic cell cycle

Bingbing Ren and others

tRNA binding to Kti12 is crucial for wobble uridine modification by Elongator

David Scherf and others

Structural Biology

Structure of the nucleosome-bound human BCL7A

Franck Martin and others

Synthetic Biology and Bioengineering

Nucleotide-level characterization and improvement of l-arabinose- and l-rhamnose-inducible systems in E. coli using a high-throughput approach

Nancy M Kim and others

De novo RNA base editing in plant organelles with engineered synthetic P-type PPR editing factors

SÃ©bastien Mathieu and others

Methods

Selict-seq profiles genome-wide off-target effects in adenosine base editing

Kexin Yuan and others

DuplexDiscoverer: a computational method for the analysis of experimental duplex RNA'RNA interaction data

Egor Semenchenko and others

pC-SAC: A method for high-resolution 3D genome reconstruction from low-resolution Hi-C data

J Carlos Angel and others

LIET model: capturing the kinetics of RNA polymerase from loading to termination

Jacob T Stanley and others

Deciphering the biosynthetic potential of microbial genomes using a BGC language processing neural network model

Qilong Lai and others

NicOPURE: nickless RNA circularization and one-step purification with engineered group II introns and cyclizing UTRs

Xiang Gao and others

Cell-cycle dependence of bursty gene expression: insights from fitting mechanistic models to single-cell RNA-seq data

Augustinas Sukys and Ramon Grima

Rapid discovery of functional RNA domains

Brandon Latifi and others

SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics

Ren-Gang Zhang and others

20th Open Access Anniversary

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