Subject: New issue: Nucleic Acids Research, Volume 53, Issue 21, 26 November 2025

Volume 53, Issue 21, 26 November 2025

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NAR Breakthrough Article

KlebPhaCol: a community-driven resource for Klebsiella research identified a novel phage family

Daniela Rothschild-Rodriguez and others

The A, B, C, D's of replicative DNA polymerase fidelity: utilizing high-throughput single-molecule sequencing to understand the molecular basis for DNA polymerase accuracy

Leonardo Betancurt-Anzola and others

Phage nuclease-mediated defense activation of the bacterial Retron-Eco7 toxin'antitoxin system

Zhikang Dai and others

Battle beyond membrane: flagella as a conduit for phage DNA entry and a trigger for bacterial defense in Yersinia enterocolitica

Zijing Wang and others

Chemical Biology and Nucleic Acid Chemistry

Impact of 2²-deoxyribo-purine substrates on nonenzymatic RNA template-directed primer extension

Ziyuan Fang and others

Crystal structure of MutYX: a novel clusterless adenine DNA glycosylase with a distinct C-terminal domain and 8-oxoguanine recognition sphere

Carlos H TrasviÃ±a-Arenas and others

CRISPR/Cas12a2 enables ultra-sensitive amplification-free RNA detection

Hyowon Jang and others

Computational Biology

Comparative assessment of physiochemical metrics for the clustering of adaptive immune receptor repertoires

Alexander A Girgis and others

Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge

Zhenhao Zhang and others

Data Resources and Analyses

The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation

Nana Ma and others

Gene Regulation, Chromatin and Epigenetics

DNA methylation dictates histone modifications in developing male germ cells in the mouse

Hirotaka Sugimoto and others

Genome Integrity, Repair and Replication

Mismatch repair disturbs meiotic crossover control in S. cerevisiae

Jon A Harper and others

Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons

Kevin Debatisse and others

Plasmodium falciparum DNA repair dynamics reveal unique roles for TLS polymerases and PfRad51 in genome diversification

Akshay Vishwanatha and others

Genomics

Distribution of DNA gyrase cleavage sites across the Streptococcus pneumoniae genome: relation to transcription and methylation at GATC sites

MarÃa-JosÃ© FerrÃ¡ndiz and others

Genome-wide ribonucleotide detection in Archaea

Yann Moalic and others

Unraveling the start element and regulatory divergence of core promoters across the domain bacteria

Syue-Ting Kuo and others

Molecular and Structural Biology

Ribonuclease toxin RelE1 inhibits growth of Mycobacterium tuberculosis through specific cleavage of the ribosomal anti-Shine'Dalgarno region

Xue Han and others

Two OB-fold proteins from a Gram-positive conjugative element engage in relaxosome assembly and DNA processing

Haifa Laroussi and others

Molecular basis of tRNA aminocarboxypropyl-transferase TapT for substrate recognition

Wei-Yan Wang and others

Nuclear DAB2IP regulates DNA replication initiation through activating PLK1-mediated HBO1 phosphorylation

Zeng-Fu Shang and others

Nucleic Acid Enzymes

Dynamics and structural features of the eEF1A1 and eEF1A2 paralogs

Oleksandra Novosylna and others

Substrate and enzyme determinants for recognition by human mitochondrial RNase P

Enxhi Hazisllari and others

Cas12a-assisted split crRNA complex for analysis and detection of diverse entities

Yao Xiao and others

Identification of determinants of high-fidelity DNA synthesis in Mycobacterium smegmatis DnaE1 through in silico and in vivo approaches

Rosan C M Kuin and others

Nucleic Acid Therapeutics

Engineered chimeric T7 RNA polymerase improves salt tolerance and reduces dsRNA impurity generation during in vitro transcription of mRNA

Athul Sanjeev and others

Biophysical and biological properties of splice-switching oligonucleotides and click conjugates containing LNA-phosphothiotriester linkages

Debashis Dhara and others

RNA and RNA-protein complexes

Chemical inhibition of exon junction complex assembly impairs mRNA localization and neural stem cells ciliogenesis

Tommaso Villa and others

A transcription termination mechanism for maintaining homogeneous protein expression

Sofia Esteban-Serna and others

The 3²'5² exoribonuclease ISG20L2 contributes to 3² terminus maturation of 18S and 28S ribosomal RNAs

Maxime Aubert and others

Diverse RNA viral effectors converge on facilitation of AGO4 degradation to promote infection

Kaili Xie and others

Structural and functional clues challenge the hypothesis that the yjdF riboswitch is natively regulated through broad recognition of azaaromatic compounds

Savannah F Spradlin and others

Synthetic Biology and Bioengineering

Metabolite-responsive scaffold RNAs for dynamic CRISPR transcriptional regulation

Anthony M Stohr and others

Methods

Coralysis enables sensitive identification of imbalanced cell types and states in single-cell data via multi-level integration

AntÃ³nio G G Sousa and others

RNA denaturation underlies circular RNA separation

Yanyi Jiang and JÃ¸rgen Kjems

Massive deciphering of the tissue nucleic acid-binding proteome via affinity chromatography integrated with data-independent acquisition-based proteomics

Huiyu Wang and others

Single-cell mapping of alternative splicing linked to checkpoint immunotherapy response

Jieyi Xiong and others

Corrections

Correction to ˜H2B.W2, a spermatocyte-specific histone variant, disrupts nucleosome stability, and reduces chromatin compaction'

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