Subject: New issue: Nucleic Acids Research, Volume 53, Issue 4, 28 February 2025

Volume 53, Issue 4, 28 February 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

Biomolecular condensation of human IDRs initiates endogenous transcription via intrachromosomal looping or high-density promoter localization

Jing Li,Shizhe Liu and others

Disassembly of unstable RNA structures by an E. coli DEAD-box chaperone accelerates ribosome assembly

Yunsheng Sun,Sarah A Woodson

Evolving a terminal deoxynucleotidyl transferase for commercial enzymatic DNA synthesis

Stephanie M Forget,Mikayla J Krawczyk and others

Critical Reviews and Perspectives

The ribosome as a platform to coordinate mRNA decay

Martin B D MÃ¼ller,Thomas Becker and others

Chemical Biology and Nucleic Acid Chemistry

Cancer cell target discovery: comparing laboratory evolution of expanded DNA six-nucleotide alphabets with standard four-nucleotide alphabets

Sharpkate Shaker,Jun Li and others

Strategic base modifications refine RNA function and reduce CRISPR'Cas9 off-targets

Kaisong Zhang,Wei Shen and others

Regulation of CRISPR trans-cleavage activity by an overhanging activator

Na Yin,Hongyan Yu and others

Computational Biology

R2DT: a comprehensive platform for visualizing RNA secondary structure

Holly McCann,Caeden D Meade and others

Precise gene expression deconvolution in spatial transcriptomics with STged

Jia-Juan Tu,Hong Yan and others

FuSViz'visualization and interpretation of structural variation using cancer genomics and transcriptomics data

Sen Zhao,Sigve Nakken and others

Shiba: a versatile computational method for systematic identification of differential RNA splicing across platforms

Naoto Kubota,Liang Chen and others

Data Resources and Analyses

Using minor variant genomes and machine learning to study the genome biology of SARS-CoV-2 over time

Xiaofeng Dong,David A Matthews and others

Gene Regulation, Chromatin and Epigenetics

A systematic survey of TF function in E. coli suggests RNAP stabilization is a prevalent strategy for both repressors and activators

Sunil Guharajan,Vinuselvi Parisutham and others

NEAT1-mediated regulation of proteostasis and mRNA localization impacts autophagy dysregulation in Rett syndrome

Edilene Siqueira,Cecilia D Velasco and others

A phosphorylation signal activates genome-wide transcriptional control by BfmR, the global regulator of Acinetobacter resistance and virulence

Nicole Raustad,Yunfei Dai and others

An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters

Yi-Hui Wang,Hannah L Hertz and others

Oncohistone H3 E97K mutation facilitates CENP-A mislocalization and chromosomal instability in budding yeast

Kentaro Ohkuni,Wei-Chun Au and others

DHX9 helicase impacts on splicing decisions by modulating U2 snRNP recruitment in Ewing sarcoma cells

Valentina Frezza,Lidia Chellini and others

A plasmid-encoded inactive toxin'antitoxin system MtvT/MtvA regulates plasmid conjugative transfer and bacterial virulence in Pseudomonas aeruginosa

Meng Li,Hua Guo and others

The NEXT complex regulates H3K27me3 levels to affect cancer progression by degrading G4/U-rich lncRNAs

Qianqian Yang,Zihan Zhou and others

Sequence-dependent and -independent effects of intron-mediated enhancement learned from thousands of random introns

Emma J K Kowal,Yuta Sakai and others

RNA exosome-driven RNA processing instructs the duration of the unfolded protein response

Laura Matabishi-Bibi,Coralie Goncalves and others

The lncRNA DUBR is regulated by CTCF and coordinates chromatin landscape and gene expression in hematopoietic cells

Hober Nelson NÃºÃ±ez-MartÃnez,Gustavo Tapia-UrzÃºa and others

Predicting gene expression from histone marks using chromatin deep learning models depends on histone mark function, regulatory distance and cellular states

Alan E Murphy,Aydan Askarova and others

The farnesoid X receptor activates transcription independently of RXR at non-canonical response elements

Suzanne W van der Veen,Jelmer J Dijkstra and others

SP140 represses specific loci by recruiting polycomb repressive complex 2 and NuRD complex

Simone Tamburri,Chiara Zucchelli and others

Phenotypic screens identify SCAF1 as critical activator of RNAPII elongation and global transcription

Pranjali Bhandare,Ashwin Narain and others

Rapid degradation of histone deacetylase 1 (HDAC1) reveals essential roles in both gene repression and active transcription

David M English,Samuel N Lee and others

PRMT1-mediated methylation regulates MLL2 stability and gene expression

Dongju An,Jihyun Kim and others

The retinoic acid family-like nuclear receptor SmRAR identified by single-cell transcriptomics of ovarian cells controls oocyte differentiation in Schistosoma mansoni

Max F Moescheid,Zhigang Lu and others

Abo1 ATPase facilitates the dissociation of FACT from chromatin

Juwon Jang,Yujin Kang and others

Centromeric localization of alpha KNL2 and CENP-C proteins in plants depends on their centromere-targeting domain and DNA-binding regions

Surya Prakash Yalagapati,Ulkar Ahmadli and others

The Staphylococcus aureus non-coding RNA IsrR regulates TCA cycle activity and virulence

Gustavo Rios-Delgado,Aubrey K G McReynolds and others

Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits

Jing Wan,Antoinette van Ouwerkerk and others

Rescuing DNMT1 fails to fully reverse the molecular and functional repercussions of its loss in mouse embryonic stem cells

Elizabeth Elder,Anthony Lemieux and others

Genome Integrity, Repair and Replication

The epigenetic landscape shapes smoking-induced mutagenesis by modulating DNA damage susceptibility and repair efficiency

Elisheva E Heilbrun,Dana Tseitline and others

Multifaceted roles of H2B mono-ubiquitylation in D-loop metabolism during homologous recombination repair

Shih-Hsun Hung,Yuan Liang and others

Oxidative damage within alternative DNA structures results in aberrant mutagenic processing

Maha Zewail-Foote,Imee M A del Mundo and others

Ubiquitin protease Ubp1 cooperates with Ubp10 and Ubp12 to revert lysine-164 PCNA ubiquitylation at replication forks

Javier ZamarreÃ±o,Sergio RodrÃguez and others

Crossovers are regulated by a conserved and disordered synaptonemal complex domain

Ana Rita Rodrigues Neves,Ivana Ä'avka and others

XRCC1 mediates PARP1- and PAR-dependent recruitment of PARP2 to DNA damage sites

Xiaohui Lin,Kay Sze Karina Leung and others

The structure of the MutL-CTD:processivity-clamp complex provides insight regarding strand discrimination in non-methyl-directed DNA mismatch repair

Shivlee Nirwal,Ritika Jha and others

Transcription-replication conflicts drive R-loop-dependent nucleosome eviction and require DOT1L activity for transcription recovery

Marcel Werner,Manuel Trauner and others

Autophosphorylation of the Tousled-like kinases TLK1 and TLK2 regulates recruitment to damaged chromatin via PCNA interaction

Kirk L West,Tram T N Nguyen and others

Phosphorylated BLM peptide acts as an agonist for DNA damage response

Ritu Agrawal,Himanshi Agarwal and others

DNA replication dynamics are associated with genome composition in Plasmodium species

Francis Isidore Garcia TotaÃ±es,Sarah E Chapman and others

Genomics

CRISPuRe-seq: pooled screening of barcoded ribonucleoprotein reporters reveals regulation of RNA polymerase III transcription by the integrated stress response via mTOR

David T Harris,Calvin H Jan

Global chromatin reorganization and regulation of genes with specific evolutionary ages during differentiation and cancer

Flavien Raynal,Kaustav Sengupta and others

The human genome encodes a multitude of novel miRNAs

Fan Gao,Fang Wang and others

Homologous recombination shapes the architecture and evolution of bacterial genomes

Ellis L Torrance,Awa Diop and others

Molecular and Structural Biology

Elevated reactive oxygen species can drive the alternative lengthening of telomeres pathway in ATRX-null cancers

Tomas Goncalves,Siobhan Cunniffe and others

Structural basis of endo-siRNA processing by Drosophila Dicer-2 and Loqs-PD

Na Cao,Jia Wang and others

Dynamics and evolutionary conservation of B complex protein recruitment during spliceosome activation

Xingyang Fu,Aaron A Hoskins

Structures of the cyanobacterial nitrogen regulators NtcA and PipX complexed to DNA shed light on DNA binding by NtcA and implicate PipX in the recruitment of RNA polymerase

Alicia Forcada-Nadal,Sirine Bibak and others

SspA is a transcriptional regulator of CRISPR adaptation in E. coli

Santiago C Lopez,Yumie Lee and others

The Vsr-like protein FASTKD4 regulates the stability and polyadenylation of the MT-ND3 mRNA

Xuan Yang,Maike Stentenbach and others

Sequestration of ribosomal subunits as inactive 80S by targeting eIF6 limits mitotic exit and cancer progression

Poonam Roshan,Aparna Biswas and others

Identification and characterization of a human MORC2 DNA binding region that is required for gene silencing

Nikole L Fendler,Jimmy Ly and others

Structural basis of ssDNA-guided NADase activation of prokaryotic SPARTA system

Rong Hu,Chenmin Guo and others

Molecular Biology

NAIL-MS reveals tRNA and rRNA hypomodification as a consequence of 5-fluorouracil treatment

Maximilian Berg,Chengkang Li and others

Nucleic Acid Enzymes

Discovery of reversing enzymes for RNA ADP-ribosylation reveals a possible defence module against toxic attack

Yang Lu,Marion Schuller and others

Inter-domain communication in the dimeric DEAD-box helicase Hera from T. thermophilus and implications for the mechanism of RNA unwinding

Pascal Donsbach,Carolin Kwas and others

Structural insights into human PNPase in health and disease

Yi-Ching Li,Chun-Hsiung Wang and others

Nucleic Acid Therapeutics

The G-quadruplex experimental drug QN-302 impairs liposarcoma cell growth by inhibiting MDM2 expression and restoring p53 levels

Beatrice Tosoni,Eisa Naghshineh and others

Virus-derived siRNA: Coronavirus and influenza virus trigger antiviral RNAi immunity in birds

Yaotang Wu,Peng Liu and others

Characterization of group I introns in generating circular RNAs as vaccines

Kuo-Chieh Liao,Majid Eshaghi and others

RNA and RNA-protein complexes

Structure of the tilapia lake virus nucleoprotein bound to RNA

BenoÃ®t Arragain,Martin Pelosse and others

ProQ-associated small RNAs control motility in Vibrio cholerae

Rabea Ghandour,Daniel Devlitsarov and others

Protein bL38 facilitates incorporation of uL6 during assembly of the 50S subunit in Flavobacterium johnsoniae

Md Siddik Alom,Dominic Arpin and others

Structural Biology

Allovalent scavenging of activation domains in the transcription factor ANAC013 gears transcriptional regulation

Elise Delaforge,Amanda D Due and others

Methods

Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data

Lingjie Liu,Yixin Zhao and others

paraCell: a novel software tool for the interactive analysis and visualization of standard and dual host'parasite single-cell RNA-seq data

Edward Agboraw,William Haese-Hill and others

Uncovering topologically associating domains from three-dimensional genome maps with TADGATE

Dachang Dang,Shao-Wu Zhang and others

A scaleable inducible knockout system for studying essential gene function in the malaria parasite

Abhinay Ramaprasad,Michael J Blackman

Synthetic anti-RNA antibody derivatives for RNA visualization in mammalian cells

Hasan Al Banna,Kimberley Berg and others

Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility

Peter Chovanec,Yi Yin

Corrections

Correction to ˜A modular toolbox for the optogenetic deactivation of transcription'

Correction to ˜Recruitment of homodimeric proneural factors by conserved CAT'CAT E-boxes drives major epigenetic reconfiguration in cortical neurogenesis'

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