Subject: New issue: Nucleic Acids Research, Volume 53, Issue 18, 14 October 2025

Volume 53, Issue 18, 14 October 2025

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NAR Breakthrough Article

Disrupted transcriptional networks regulated by CHD1L during neurodevelopment underlie the mirrored neuroanatomical and growth phenotypes of the 1q21.1 copy number variant

Marianne Victoria LemÃ©e and others

Critical Reviews and Perspectives

On the origin, evolution, and maintenance of RNA editing

Yuange Duan and others

Translational and clinical development of therapeutic siRNA and ASOs: current industry practices, perspectives, and recommendations

Jesper Kammersgaard Christensen and others

Chemical Biology and Nucleic Acid Chemistry

Modified unlocked nucleic acid (MUNA) mitigates off-target effects of small interfering RNAs

Shohei Mori and others

Click DNA ligation with deoxyribozyme

Yangyang Chang and others

A quantitative model of enzyme-free copying of RNA with dimers

Ludwig Burger and others

Computational Biology

SPACE: Spatially variable gene clustering adjusting for cell type effect for improved spatial domain detection

Sikta Das Adhikari and others

Structural and evolutionary determinants of Argonaute function

Arndt Wallmann and Mathew Van de Pette

Systematic identification of regions where DNA methylation is correlated with transcription refines regulatory logic in normal and tumour tissues

Richard Heery and Martin H Schaefer

Ultra-fast variant effect prediction using biophysical transcription factor binding models

Rezwan Hosseini and others

Data Resources and Analyses

Spatiotemporal dynamics and selectivity of mRNA translation during mouse pre-implantation development

Hao Ming and others

Gene Regulation, Chromatin and Epigenetics

Mammalian H4K16ac regulates the spatiotemporal order of genome replication rather than gene expression

Marta Milan and others

Abundant bacterial nucleoid-associated protein H-NS limits plasmid transfer through mechanical modification of DNA

Mingyue Fei and others

Reactive sulfur species mediated persulfidation cascade regulation mechanism of novel transcription factor SscR^Ac in extremophile Acidithiobacillus caldus under extreme copper stress

Xingyu Huo and others

Dam-dependent epigenetic memory regulates prophage reintegration in Salmonella

Jihye Yang and others

ARID1A regulates histone octamer transfer activity of human canonical BAF complex

Naoe Moro and others

WDR5 serves in co-activation and influences genome targeting of KLF3

Lu Yang and others

The arabidopsis GyraseB3 contributes to transposon silencing by promoting histone deacetylation

Isabelle Gy and others

Teamwork of clustered low-affinity kappa B sites and accessory factors regulates transcriptional strength of NF-kappa B RelA dimers

Shandy Shahabi and others

KAT5-mediated acetylation of PC4 facilitates DNA repair by promoting chromatin reorganization

Aayushi Agrawal and others

Genome Integrity, Repair and Replication

DNA polymerase kappa is the primary translesion synthesis polymerase for aldehyde ICLs

Roxanne V van der Sluijs and others

RNA/DNA-binding protein TDP43 regulates DNA mismatch repair genes with implications for genome stability

Vincent E Provasek and others

ATRX cooperates with TOP2B for replication fork stability and DNA damage response through G-quadruplex regulation

Ying Pang and others

Damage-induced phosphorylation of BRC-1/BRD-1 in meiosis preserves germline integrity

Nuria FernÃ¡ndez-FernÃ¡ndez and others

RNF4 and USP7 coordinate spatial regulation of SLX4 stability within the PML nuclear bodies

Eunyoung Jung and others

Residues in the little finger domain of the Y-family Dpo4 DNA polymerase communicate to restrict synthesis past 8-oxoguanine lesions

Sadia Sinty Disha and others

Leading and lagging strand abasic sites differentially affect vertebrate replisome progression but involve analogous bypass mechanisms

Matthew T Cranford and others

KRAS-induced STN1 (OBFC1) promotes proper CTC1'STN1'TEN1 complex-independent DNA double-strand break repair and cell cycle checkpoint maintenance in pancreatic cancer

Changxian Shen and others

GASZ directly recruits MILI to the intermitochondrial cement for piRNA biogenesis and male germ cell development

Junru Miao and others

Genomics

The early injected genomic region determines sensitivity to Type I restriction-modification defence against Autographiviridae phages

Andrea Martinez-Cazorla and others

Coordinated control of genome'nuclear lamina interactions by topoisomerase 2B and lamin B receptor

Tom van Schaik and others

Molecular and Structural Biology

Opposing roles of two R-loop associated G-quadruplexes in tuning transcription activity

Leya Yang and others

Engineering of BZ transposase and transposon donor vector for enhanced efficiency and safety in gene delivery applications

Saisai Wang and others

Novel fold and wing structure of Forkhead transcription factor facilitate DNA binding

George L Wang and others

The ParB-CTP cycle activates phase separation in bacterial DNA segregation

Linda Delimi and others

Eps2Fold: a rapid method to characterize G-quadruplex DNA structures using single absorbance spectra

Eric Largy and others

Mechanistic insights into Cas13d enzymes from cryo-EM structures of CasRx and DjCas13d

Xiaoyan Chen and others

New structural insights into the control of the retinoic acid receptors RAR/RXR by DNA, ligands, and transcriptional coregulators

Izabella Tambones and others

Nucleic Acid Enzymes

Rapid CRISPR'Cas9 target-strand nicking can provide phage resistance by reducing DNA abundance

Giang T Nguyen and others

Molecular interplay between ComEC domains allows for selective degradation of the non-translocating strand during natural transformation

Matthew J M Stedman and others

Stable Cas9 expression regulates cell growth by facilitating mTORC2 activation

Le Yu and others

A multi-dentate, cooperative interaction between endo- and exo-ribonucleases within the bacterial RNA degradosome

Giulia Paris and others

CRISPR-Cas12a REC2'Nuc interactions drive target-strand cleavage and constrain trans cleavage

Anthony Newman and others

RNA and RNA-protein complexes

DHX36 modulates stress granule assembly independent of recruitment of mRNAs with G-quadruplex sequence motifs

Li Yi Cheng and others

Angel wing: a class of alternative splicing regulators in animals

Ting Zhang and others

Iron-sensitive RNA regulation by poly C-binding proteins

Grant A Goda and others

Canonical translation factors eIF1A and eIF5B modulate the initiation step of repeat-associated non-AUG translation

Hayato Ito and others

Plant-specific BLISTER modulates miRNA biogenesis by regulating MIR transcription, HYL1 phosphorylation, and nuclear transport in Arabidopsis

Shu Wang and others

Synthetic Biology and Bioengineering

Metagenome-inspired libraries to engineer phage M13 for targeted killing of Gram-negative bacterial species

Yanxi Yang and others

High-efficiency homology-directed insertion into the genome using the engineered homing endonuclease ARCUS

Laura Christian Resly and others

Methods

Comprehensive profiling of activity and specificity of RNA-guided transposons reveals opportunities to engineer improved variants

Seong Guk Park and others

Base-resolution profiling of 5-glyceryl-methylcytosine in Chlamydomonas reinhardtii via deaminase-assisted sequencing

Fan-Chen Wang and others

On metrics for subpopulation detection in single-cell and spatial omics data

Siyuan Luo and others

gwSPADE: gene frequency-weighted reference-free deconvolution in spatial transcriptomics

Aoqi Xie and others

MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis

Yan Xia and others

Corrections

Correction to ˜Re-establishment of H3K9me2 eliminates the transcriptional inhibition of ST18 on meiotic genes and orchestrates female germ cell development'

Correction to ˜The Shu complex promotes error-free tolerance of alkylation-induced base excision repair products'

Correction to ˜Small molecules inhibitors of the heterogeneous ribonuclear protein A18 (hnRNP A18): a regulator of protein translation and an immune checkpoint'

Editor's Note

Editor's Note on ˜Mutagenesis of human DNA polymerase lambda : essential roles of Tyr505 and Phe506 for both DNA polymerase and terminal transferase activities'

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