Subject: New issue: Nucleic Acids Research, Volume 53, Issue 14, 12 August 2025

Volume 53, Issue 14, 12 August 2025

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NAR Breakthrough Article

Evidence that transient replication errors initiate nuclear genome mutations

Scott A Lujan and others

Identification of cognate recombination directionality factors for large serine recombinases by virtual pulldown

Heewhan Shin and others

tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa

Jingjing Sun and others

Spontaneously directed loop extrusion in SMC complexes emerges from broken detailed balance and anisotropic DNA search

Andrea Bonato and others

Capturing a glycosylase reaction intermediate in DNA repair by freeze-trapping of a pH-responsive hOGG1 mutant

Masaki Unno and others

Critical Reviews and Perspectives

The extended mobility of plasmids

Maria Pilar GarcillÃ¡n-Barcia and others

Prevalence of errors in lab-made plasmids across the globe

Xingjian Bai and others

Chemical Biology and Nucleic Acid Chemistry

ModiDeC: a multi-RNA modification classifier for direct nanopore sequencing

NicolÃ² Alagna and others

tRNA hydroxylation is an epitranscriptomic modulator of metabolic states affecting Pseudomonas aeruginosa pathogenicity

Yannick N Frommeyer and others

An enhanced Eco1 retron editor enables precision genome engineering in human cells without double-strand breaks

Matthew A Cattle and others

Cyclic tetraadenylate binding induces dimerization of protein dimers to activate a CRISPR-associated PIN nuclease

Fang Wang and others

Computational Biology

Untargeted CUT&Tag reads are enriched at accessible chromatin and restrict identification of potential G4-forming sequences in G4-targeted CUT&Tag experiments

Matthew D Thompson and Alicia K Byrd

Learning interpretable representations of single-cell multi-omics data with multi-output Gaussian processes

Zahra Moslehi and others

Nucleosome placement and polymer mechanics explain genomic contacts on 100 kb scales

John Corrette and others

ExcludonFinder: mapping transcriptional overlaps between neighboring genes

Ã lvaro SanmartÃn and others

Proteogenomics-enabled discovery of novel small open reading frame (sORF)-encoded polypeptides in human and mouse tissues

Mei Yang and others

SnoBIRD: a tool to identify C/D box snoRNAs and refine their annotation across all eukaryotes

Ã‰tienne Fafard-Couture and others

Data Resources and Analyses

A side-by-side comparison of variant function measurements using deep mutational scanning and base editing

Ivan Sokirniy and others

Gene Regulation, Chromatin and Epigenetics

BAHCC1 promotes gene expression in neuronal cells by antagonizing SIN3A'HDAC1

Alan Monziani and others

Mouse metastable epialleles are extremely rare

Chathura J Gunasekara and others

The ISPpu9 insertion sequence of Pseudomonas putida KT2440 generates various circular intermediates enabling modular transposition

Elena ParÃ©s-GuillÃ©n and others

PPARG-centric transcriptional re-wiring during differentiation of human trophoblast stem cells into extravillous trophoblasts

Qingqing Guo and others

Widespread 3² UTR splicing regulates expression of oncogene transcripts through multiple mechanisms

Jack J Riley and others

A U3 snoRNA is required for the regulation of chromatin dynamics and antiviral response in Drosophila melanogaster

Shruti Jain and others

SUMO operates from a unique long tandem repeat to keep innate immunity in check

Amandine Goffeney and others

Autoregulation of RPL7B by inhibition of a structural splicing enhancer

David Granas and others

Liquid'liquid phase separation of lamin drives altered chromatin organization in cardiomyopathic mutations of lamin A

Subhradip Nath and others

AlphaFold-guided structural analyses of nucleosome binding proteins

Xin Yang and others

Genome Integrity, Repair and Replication

SWI5'SFR1 reduces RAD51 recombinase extending units during filament assembly

Yingying Hu and others

FEN1 is critical for rapid single-strand break repair in G1 phase

Kamila Burdova and others

Methylglyoxal mutagenizes single-stranded DNA via Rev1-associated slippage and mispairing

Sriram Vijayraghavan and others

Recombination-coupled DNA synthesis facilitates post-invasion steps in meiotic crossover and noncrossover formations

Hyungseok Choi and others

SMUG1 DNA glycosylase modulates reward behaviour through regulation of olfactory receptor gene expression

Diana L Bordin and others

Late steps of allelic break-induced replication suppress tandem duplication associated with BRCA1 deficiency

Zhi-Cheng Huang and others

The function of MYC in base excision repair protects against RAS-induced senescence

Camila C F Faraco and others

The B. subtilis replicative polymerases bind the sliding clamp with different strengths to tune their activity in DNA replication

Luke G O'Neal and others

S-phase checkpoint protects from aberrant replication fork processing and degradation

IvÃ¡n NÃºÃ±ez-MartÃn and others

ecDNA replication is disorganized and vulnerable to replication stress

Jedrzej J Jaworski and others

Genome-wide mapping of formaldehyde-induced DNA'protein crosslinks reveals unique patterns of formation and transcription-coupled removal in mammalian cells

Duha Alshareef and others

Genomics

Low-amplitude copy number gains shape cancer through known and novel oncogenes with associated therapeutic vulnerabilities

Thomas F Eleveld and others

Quantitative modeling of mRNA degradation reveals tempo-dependent mRNA clearance in early embryos

Mazal Tawil and others

Molecular and Structural Biology

Structural basis for sensitivity and acquired resistance of fungal cap guanine-N7 methyltransferases to the antifungal antibiotic sinefungin

Daniel J Nilson and others

A phage transcription factor displaces the host Ïƒ factor and stabilizes its own Ïƒ factor

Liqiao Xu and others

The structure, folding kinetics, and dynamics of long poly(UG) RNA

Riley J Petersen and others

Temperature-dependent funnel-like DNA folding landscapes

Marc Rico-Pasto and others

Molecular mechanisms of biomolecular condensate formation in Drosophila melanogaster siRNA biogenesis

Clara Hipp and others

The evolution of eukaryotic linear motifs governing the function of androgen receptor from fish to Homo sapiens

Antonella Falconieri and others

Identification of regulatory sequences in Aca11 and Aca13 for detection of anti-CRISPR and protein'protein interaction

Guoxu Song and others

Crystal structures reveal the distinct features of the 2²-dG-III riboswitch in the purine riboswitch family

Ke Chen and others

Noncanonical RNA binding of human La-related protein 6

Blaine H Gordon and others

Altered mRNA transport and local translation in i³Neurons with RNA-binding protein knockdown

Rachael Dargan and others

G-quadruplexes as potential traps for superenhancer marker BRD4: ligand-sensitive binding and co-separation in vitro

Iuliia I Pavlova and others

SEISMICgraph: a web-based tool for RNA structure data visualization

Federico Fuchs Wightman and others

Structural basis of nucleosome binding and destabilization by the extended DNA binding domain of RFX5

Wanqiang Xue and others

Structural and functional characterization of CspR, a 2²-O-methyltransferase acting on wobble position within tRNA

Jaehun Yoo and others

Structural basis for small molecule binding to the SARS-CoV-2 nsp10'nsp14 ExoN complex

Frank Kozielski and others

MexR and NalD are pyocyanin-responsive transcriptional repressors of the efflux pump MexAB-OprM in Pseudomonas aeruginosa

Cancan Wu and others

Structural and mechanistic insights into the transcriptional regulation of chromosomal T6SS by large conjugative plasmid-encoded TetRs in Acinetobacter baumannii

Wenbo He and others

Nucleic Acid Enzymes

Unleashing high trans-substrate cleavage kinetics of Cas12a for nucleic acid diagnostics

Eric A Nalefski and others

DNA large fragment deleting by compact, sequence-motif-free and specific TaqTth-hpRNA assisted with the microhomology-mediated end joining pathway

Yu Liu and others

Nucleic Acid Therapeutics

Single alkyl phosphonate modification of the siRNA backbone in the seed region enhances specificity and therapeutic profile

Mehran Nikan and others

High-fidelity and differential nonsense suppression in live cells and a frontotemporal dementia allele with human transfer RNAs

Aruun Beharry and others

RNA and RNA-protein complexes

Identification and characterization of shifted G¢U wobble pairs resulting from alternative protonation of RNA

Md Sharear Saon and others

SARS-CoV-2 Nsp2 recruits GIGYF2 near viral replication sites and supports viral protein production

Jimi Kim and others

Rapid depletion and super-resolution microscopy reveal dual roles of SRSF5 in coordinating nuclear speckle'paraspeckle crosstalk during cellular stress

Ellen Kazumi Okuda and others

RNA adapts its flexibility to efficiently fold and resist unfolding

Sukjin S Jang and others

Trichothiodystrophy-causative pathogenic variants impair a cooperative action of TFIIH and DDX1 in R-loop processing

Debora Ferri and others

The type 6 secretion system immunity protein RhsFI has been repurposed for small RNA regulation in pathogenic Escherichia coli

Thomas Zammit and others

Base-resolution binding profile prediction of proteins on RNAs with deep learning

Xiaojian Liu and others

Synthetic Biology and Bioengineering

A quorum sensing-controlled type I CRISPRi toolkit for dynamically regulating metabolic flux

Han Zheng and others

Genetic "expiry-date" circuits control lifespan of synthetic scavenger bacteria for safe bioremediation

Kha Mong Tran and others

Synthetic G-quadruplex components for predictable, precise two-level control of mammalian recombinant protein expression

Melinda Pohle and others

Electro-switchable addressing system for achieving repetitive random data access

Haotian Yu and others

Methods

Automated high-throughput profiling of single-cell total transcriptome with scComplete-seq

Fatma BetÃ¼l DinÃ§aslan and others

SMAdd-seq: probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing

Gali Bai and others

Spatial-scERA: a method for reconstructing spatial single-cell enhancer activity in multicellular organisms

Baptiste Alberti and others

A cluster-based cell-type deconvolution of spatial transcriptomic data

Qingyue Wang and others

Direct histone proteoform profiling of the unannotated, endangered coral Acropora cervicornis

Cassandra N Fuller and others

Unlocking genetic potential: harnessing phage for targeted mutagenesis in phage-assisted evolution

Maryam Ali and others

A versatile anti-CRISPR platform for opto- and chemogenetic control of CRISPR-Cas9 and Cas12 across a wide range of orthologs

Luca Brenker and others

Corrections

Correction to ˜The N = 1 Collaborative: advancing customized nucleic acid therapies through collaboration and data sharing'

Correction to 'Stacking correlation length in single-stranded DNA'

Correction to ˜A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei'

Correction to ˜proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms'

Correction to ˜Exploration and analysis of R-loop mapping data with RLBase'

Correction to ˜Selective disruption of an oncogenic mutant allele by CRISPR/Cas9 induces efficient tumor regression'

Correction to ˜Cytoplasmic and nuclear quality control and turnover of single-stranded RNA modulate post-transcriptional gene silencing in plants'

Editor's Note

Editor's Note on ˜Error-free bypass of 2-hydroxyadenine by human DNA polymerase lambda with Proliferating Cell Nuclear Antigen and Replication Protein A in different sequence contexts'

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