Subject: New issue: Nucleic Acids Research, Volume 53, Issue 19, 28 October 2025

Volume 53, Issue 19, 28 October 2025

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NAR Breakthrough Article

Direct observation of interdependent and hierarchical kinetochore assembly on individual centromeres

Changkun Hu and others

Critical Reviews and Perspectives

Knowing is not enough; we must apply: the case for rigorous microRNA annotation standards

Michael Hackenberg and others

Chemical Biology and Nucleic Acid Chemistry

Single-colony resolution of CRISPR'Cas adaptation in E. coli reveals altered spacer-source bias during solid-phase growth

Jack Braithwaite and others

Targeting DNA termini with a small-molecule natural product analogue: a DNA end-binder (DEB) to augment DNA double-strand breaks

Nikhil Tuti and others

Computational Biology

GQ-DNABERT reveals GQ proximal enhancer'promoter interactions associated with tissue-specific transcription

Dmitry Konovalov and others

Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard

Yu-Yu Lin and others

Data Resources and Analyses

The knock-in atlas: a web resource for targeted protein trap by CRISPR/Cas9 in human and mouse cell lines

Yuma Hanai and others

Gene Regulation, Chromatin and Epigenetics

Using single-cell perturbation screens to decode the regulatory architecture of splicing factor programs

Miquel Anglada-Girotto and others

The homeobox transcription factor MNX1 regulates the expression of many non-MN-specific neuronal genes in motor neurons

Ming-an Sun and others

Adsorption of phage T2 is inhibited due to inversion of cryptic prophage DNA by the serine recombinase PinQ

Joy Kirigo and others

Allele-specific genomics decodes gene targets and mechanisms of the non-coding genome

Tim P Hasenbein and others

A non-coding role for trypanosome VSG transcripts in allelic exclusion

Douglas O Escrivani and others

Refined mechanism of promoter nucleosome-depleted regions resetting after replication

Sevil Zencir and others

Genome Integrity, Repair and Replication

Ligase 3 prevents oxidative strand break-induced mitochondrial DNA loss but is not essential for replicative circularization

Genevieve Trombly and others

Distinct roles of RECQL5 in RAD51-mediated fork reversal and transcription elongation

Tarun Nagraj and others

Decoding nucleoside supplementation: how thymidine outperforms ribonucleosides in accelerating mammalian replication forks

Praveen Pandey and others

A histone methyltransferase-independent function of PRC2 controls small RNA dynamics during programmed DNA elimination in Paramecium

Caridad MirÃ³-Pina and others

Bloom helicase contributes to successful crossover formation with both catalytic and structural roles in Caenorhabditis elegans meiosis

Sowmya Sivakumar Geetha and others

Structural insights into gamma H2Ax containing nucleosomes

Rashmi Panigrahi and others

MazF endoribonuclease promotes resolution of transcription'replication conflicts at ribosomal RNA genes in Escherichia coli

Sebastien Fleurier and Ivan Matic

Molecular and Structural Biology

Expanding the HP1a-binding consensus and molecular grammar for heterochromatin assembly

Serafin U Colmenares and others

Structural basis of enhanced stalling efficiency of an engineered ribosome arrest peptide

Manoj Kumar Sriramoju and others

Helical correlations in curved DNA condensates

Kahina Vertchik and others

Molecular insights into the Drosophila piRNA pathway via systematic ReLo protein interaction screening and structure prediction

Harpreet Kaur Salgania and others

Structural basis of multitasking by the apicoplast DNA polymerase from Plasmodium falciparum

Anamika Kumari and others

The Kaposi's sarcoma-associated herpesvirus TBP mimic uses a noncanonical DNA-binding mode to promote viral late gene transcription

Lidia E Llacsahuanga-Allcca and others

Nucleoid structure and dynamics influence natural chromosomal transformation in Bacillus subtilis: the role of EbfC

RubÃ©n Torres and others

The multimerization pathway of the glucocorticoid receptor

Andrea Alegre-MartÃ and others

The herpes simplex origin-binding protein: mechanisms for sequence-specific DNA binding and dimerization revealed by Cryo-EM

Emil Gustavsson and others

DNA-bound structure of Clostridioides difficile heme-sensing HsmR gives insight on how the unique dimer mode governs DNA specificity in MarR transcriptional regulators

SooHo Rho and others

Nucleic Acid Therapeutics

MiR-ON-CRISPR: a microRNA-activated CRISPR'dCas9 system for precise gene therapy in living cells and mouse models of sepsis

Wen-Jie Shu and others

RNA and RNA-protein complexes

The organization principles of P. falciparum translation initiation features and their potential as drug targets

Rom Barzilay and others

Codon specific readthrough as a mechanism of BRCA2 restoration in acquired PARP inhibitor and chemotherapy resistance

Cordelia D McGehee and others

High-throughput single-virion DNA-PAINT reveals structural diversity, cooperativity, and flexibility during selective packaging in influenza

Christof Hepp and others

Dysregulation of AGO2-miRNA dynamics underlies the AGO2-associated Lessel'Kreienkamp syndrome

TingYu M Liu and others

Functional microRNA targeting without seed pairing

Matthew H Hall and others

N1-methylpseudouridine mRNA modification enhances efficiency and specificity of gene overexpression by preventing Prkra-mediated global translation repression

Tong Lu and others

mRNA turnover dynamics are affected by cell differentiation and loss of the cytosine methyltransferase Nsun2

Isabel Delazer and others

Condensation of the RNA chaperone Hfq is coupled to inhibition of glucose uptake and contributes to the stabilization of regulatory RNAs in nitrogen-starved Escherichia coli

Josh McQuail and others

The intrinsic properties of mRNAs define their translation efficiency at ribosome shortage

Elena S Babaylova and others

Methods

A versatile platform for combinatorial antibody library cloning and NGS-based quality control with high accuracy

Zhongyao Zhang and others

Mapping transcription factor binding sites by learning UV damage fingerprints

Hannah E Wilson and others

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