Subject: New issue: Nucleic Acids Research, Volume 53, Issue 5, 24 March 2025

Volume 53, Issue 5, 24 March 2025

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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

ProQ prevents mRNA degradation through inhibition of poly(A) polymerase

Sofia Bergman,Christopher Birk and others

A new level of RNA-based plant protection: dsRNAs designed from functionally characterized siRNAs highly effective against Cucumber mosaic virus

Marie Knoblich,Torsten Gursinsky and others

Critical Reviews and Perspectives

Molecular mechanisms of extrachromosomal circular DNA formation

Rasmus A B Eugen-Olsen,Judith M Hariprakash and others

Toward the use of nanopore RNA sequencing technologies in the clinic: challenges and opportunities

Xanthi-Lida Katopodi,Oguzhan Begik and others

Chemical Biology and Nucleic Acid Chemistry

Crosslinking pathways, dynamics, and kinetics between guanosine and lysine following one- versus two-electron oxidation of guanosine

May Myat Moe,Jonathan Benny and others

Z-form DNA-RNA hybrid blocks DNA replication

Shiyu Wang,Yan Xu

Chemical evolution of ASO-like DNAzymes for effective and extended gene silencing in cells

Yingyu Liu,Sheyu Zhang and others

Fluorogenic oligonucleotide cleavage probes with a branched linker improve RNA detection

Bruktawit Maru,Ayodele Edinboro and others

Zwitterionic DNA: enzymatic synthesis of hypermodified DNA bearing four different cationic substituents at all four nucleobases

Natalia Kuprikova,Marek OndruÅ¡ and others

A novel L-RNA aptamer to regulate the pUG fold RNA-induced gene expression in vivo

Shiau Wei Liew,Dong Cao and others

Enhanced or reversible RNA N6-methyladenosine editing by red/far-red light induction

Heng Tang,Shaoqin Han and others

Imperfect G-quadruplex as an emerging candidate for transcriptional regulation

Sunipa Sarkar,Hisae Tateishi-Karimata and others

Computational Biology

A detailed analysis of second and third-generation sequencing approaches for accurate length determination of short tandem repeats and homopolymers

Sophie I Jeanjean,Yimin Shen and others

Deep learning-based cell-specific gene regulatory networks inferred from single-cell multiome data

Junlin Xu,Changcheng Lu and others

DNAcycP2: improved estimation of intrinsic DNA cyclizability through data augmentation

Brody Kendall,Chong Jin and others

Gene Regulation, Chromatin and Epigenetics

Argonaute CSR-1A promotes H3K9me3 maintenance to protect somatic development in offspring

Di Rao,Dengfeng Li and others

A noncanonical intrinsic terminator in the HicAB toxin'antitoxin operon promotes the transmission of conjugative antibiotic resistance plasmids

Jianzhong Lin,Songwei Ni and others

A transcription factor from the cryptic Escherichia coli Rac prophage controls both phage and host operons

Ewa Wons,Katarzyna Gucwa and others

Deletion of Xist repeat B disrupts cell cycle and asymmetric cell division through Usp9x hyperactivation in mice

Mingming Liang,Lichao Zhang and others

Checkpoint kinases regulate the circadian clock after DNA damage by influencing chromatin dynamics

Yulin Yang,Zeyu Duan and others

Transcriptional mechanism by which IS5 activates the fucAO operon in Escherichia coli

Harry Zhou,Zhongge Zhang and others

Transcription factor VIB-1 activates catalase-3 expression by promoting PIC assembly in Neurospora crassa

Huan Liu,Qin Zhang and others

Genome-wide transcriptional silencing and mRNA stabilization allow the coordinated expression of the meiotic program in mice

Laura Bellutti,Edith Chan Sock Peng and others

Overlapping and distinct functions of SPT6, PNUTS, and PCF11 in regulating transcription termination

Fabienne Bejjani,Emmanuel SÃ©gÃ©ral and others

Genome Integrity, Repair and Replication

Mug20'Rec25'Rec27 binds DNA and enhances meiotic DNA break formation via phase-separated condensates

Max F Wang,Meng-Yun Li and others

Mono-ubiquitination of TopBP1 by PHRF1 enhances ATR activation and genomic stability

Fei Zhao,Chenghui Cai and others

The mutational landscape of Bacillus subtilis conditional hypermutators shows how proofreading skews DNA polymerase error rates

Ira Tanneur,Etienne Dervyn and others

Armadillo domain of ARID1A directly interacts with DNA-PKcs to couple chromatin remodeling with nonhomologous end joining (NHEJ) pathway

Shin-ichiro Kanno,Takayasu Kobayashi and others

Rapid dynamics allow the low-abundance RTEL1 helicase to promote telomere replication

Guanhui Wu,Erin Taylor and others

APE1 condensation in nucleoli of non-cancer cells depends on rRNA transcription and forming G-quadruplex RNA structures

Giuseppe Dall'Agnese,Nancy M Hannett and others

MutLgamma enforces meiotic crossovers in Arabidopsis thaliana

StÃ©phanie Durand,Qichao Lian and others

Genetic dissection of MutL complexes in Arabidopsis meiosis

Nadia Kbiri,Nadia FernÃ¡ndez-JimÃ©nez and others

DNA damage response regulator ATR licenses PINK1-mediated mitophagy

Christian Marx,Xiaobing Qing and others

A conserved thumb domain insertion in DNA polymerase epsilon supports processive DNA synthesis

Sohail Ahmad,Siying Zhang and others

Genomics

Self-splicing introns in genes of Bastillevirinae bacteriophages

Martyna WÄ™glewska,Joanna Gracz-Bernaciak and others

Molecular and Structural Biology

Conformational reorganization and phase separation drive hyper-editing of ADR-2'ADBP-1 complex

Jianqiang Mu,Cang Wu and others

Structural basis for cooperative ssDNA binding by bacteriophage protein filament P12

Lena K TrÃ¤ger,Morris Degen and others

Eukaryotic initiation factors eIF4F and eIF4B promote translation termination upon closed-loop formation

Ekaterina Shuvalova,Alexey Shuvalov and others

Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells

Jason R Stagno,Justin C Deme and others

Structural basis of TnsC oligomerization and transposase recruitment in type I-B CRISPR-associated transposons

Giada Finocchio,Irma Querques and others

VirBR counter-silences HppX3 to promote conjugation of bla_NDM-IncX3 plasmids

Yuan Gao,Ning Xie and others

Nucleic Acid Enzymes

Structural basis for aminoacylation of cellular modified tRNA^Lys3 by human lysyl-tRNA synthetase

Swapnil C Devarkar,Christina R Budding and others

Systematic analysis of specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases reveals mechanisms of enzyme- and sequence-specific DNA readout

Greta Sogl,Sabrina Pilling and others

Mitochondrial exonuclease EXOG supports DNA integrity by the removal of single-stranded DNA flaps

Anna Karlowicz,Andrzej B Dubiel and others

Nucleic Acid Therapeutics

Packaged delivery of CRISPR'Cas9 ribonucleoproteins accelerates genome editing

Hannah Karp,Madeline Zoltek and others

Tuning the tropism and infectivity of SARS-CoV-2 virus-like particles for mRNA delivery

Qi Yang,Bruce A Davidson and others

RNA and RNA-protein complexes

The snoRNP chaperone snR190 and the Npa1 complex form a macromolecular assembly required for 60S ribosomal subunit maturation

Hussein Hamze,Mariam Jaafar and others

Amyloid-like DNA bridging: a new mode of DNA shaping

Frank Wien,Marcos Gragera and others

Yeast poly(A)-binding protein (Pab1) controls translation initiation in vivo primarily by blocking mRNA decapping and decay

Poonam Poonia,Vishalini Valabhoju and others

Deciphering the landscape of cis-acting sequences in natural yeast transcript leaders

Christina Akirtava,Gemma E May and others

RNA anchoring of Upf1 facilitates recruitment of Dcp2 in the NMD decapping complex

Nadia Ruiz-Gutierrez,Jeanne Dupas and others

Small molecule inhibitors of hnRNPA2B1'RNA interactions reveal a predictable sorting of RNA subsets into extracellular vesicles

Jessica Corsi,Pouriya Sharbatian Semnani and others

Ribosome stalling-induced NIP5;1 mRNA decay triggers ARGONAUTE1-dependent transcription downregulation

Mayuki Tanaka,Naoyuki Sotta and others

Syn-tasiR-VIGS: virus-based targeted RNAi in plants by synthetic trans-acting small interfering RNAs derived from minimal precursors

Adriana E Cisneros,Ana Alarcia and others

Structural Biology

Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism

Vito Genna,Guillem Portella and others

Synthetic Biology and Bioengineering

Decoding and reengineering the promoter specificity of T7-like RNA polymerases based on phage genome sequences

Jinwei Zhu,Ziming Liu and others

Engineering oxypurinol-responsive riboswitches based on bacterial xanthine aptamers for gene expression control in mammalian cell culture

Vera Hedwig,Maike SpÃ¶ring and others

Methods

Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses

Kathryn Langenfeld,Bridget Hegarty and others

Quantification of subcellular RNA localization through direct detection of RNA oxidation

Hei-Yong G Lo,Raeann Goering and others

stAI: a deep learning-based model for missing gene imputation and cell-type annotation of spatial transcriptomics

Guangsheng Zou,Qunlun Shen and others

In silico lambda -dynamics predicts protein binding specificities to modified RNAs

Murphy Angelo,Wen Zhang and others

Transcriptome-wide mapping of N³-methylcytidine modification at single-base resolution

Yunyi Gao,Jingyu Hou and others

Optimizing gRNA selection for high-penetrance F0 CRISPR screening for interrogating disease gene function

Sheng-Jia Lin,Kevin Huang and others

Corrections

Correction to ˜Functional redundancy in tRNA dihydrouridylation'

Correction ˜LncPepAtlas: a comprehensive resource for exploring the translational landscape of long non-coding RNA'

Correction to ˜Inhibition of HMGA2 binding to AT-rich DNA by its negatively charged C-terminus'

Correction to ˜iDog: a multi-omics resource for canids study'

Correction to ˜Structural characterization of two prototypical repressors of SorC family reveals tetrameric assemblies on DNA and mechanism of function'

Correction to ˜Chromosomal integrons are genetically and functionally isolated units of genomes'

Correction to ˜WBSCR16 is Essential for Mitochondrial 16S rRNA Processing in Mammals'

Correction to ˜RNPC1 modulates the RNA-binding activity of, and cooperates with, HuR to regulate p21 mRNA stability'

Correction to ˜DisProt in 2024: improving function annotation of intrinsically disordered proteins'

Editor's Note

Editor's Note on ˜A regulatory circuit comprising GATA1/2 switch and microRNA-27a/24 promotes erythropoiesis'

This email is intended for bionet@evol.mcmaster.ca.