Subject: New issue: Nucleic Acids Research, Volume 53, Issue 22, 11 December 2025

Volume 53, Issue 22, 11 December 2025

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Matters Arising

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

Larry Melidis and others

Response to the commentary by Melidis et al. on "Untargeted CUT&Tag reads are enriched at accessible chromatin and restrict identification of potential G4-forming sequences in G4-targeted CUT&Tag experiments"

Alicia K Byrd and Matthew D Thompson

NAR Breakthrough Article

A trypanosome-specific complex mediates late-stage processing of cytosolic LSU rRNA

Simona Amodeo and others

Crystal structure of the class V GTP-binding RNA aptamer bound to its ligand: GTP recognition by a topologically complex intermolecular G-quadruplex

Helena Stafflinger and others

Suboptimal codon pairs trigger ribosome collisions and cellular quality control responses in tRNA modification mutants

Jie Wu and others

Critical Reviews and Perspectives

Eukaryotic translation initiation factor 4F: functional properties and physiological role

Ekaterina Shuvalova and others

The CCR4'NOT complex: a multifaceted sensor of molecular signals instructing eukaryotic mRNA translation and stability

Guillaume Caulier and others

Chemical Biology and Nucleic Acid Chemistry

Modulating TERRA G-quadruplexes with ligands: impact on telomeric DNA:RNA hybrids and ALT mechanisms

Federico Dinoi and others

Direct RNA sequencing enables improved transcriptome assessment and tracking of RNA modifications for medical applications

Charlotte Hewel and others

Deciphering the intermolecular interactions between G-quadruplex (G4)-forming sequences

Jianjun Xia and others

Fluorescent modifications in aptamer switches'positional, structural, and neighboring pair effects on sensor performance

Albert Zehan Li and others

Amplification-free cancer diagnosis based on inhibition of Cas12a activity by site-specific 5mC-modified cfDNA

Feng Yang and others

Helical aromatic oligoamide foldamers as selective G-quadruplex ligands

Alexander KÃ¶nig and others

Computational Biology

Integrative and accurate annotations enhance current nonsense-mediated mRNA decay rules

Hiroyuki Iha and others

DNA shape and epigenomics distinguish the mechanistic origin of human genomic structural variations

Nadejda B Boev and others

Influence of contact map topology on RNA structure prediction

Christian Faber and others

Gene Regulation, Chromatin and Epigenetics

Base composition at the start of the coding sequence controls the balance between translation initiation and mRNA degradation in E. coli

Anna LipoÅ"ska and others

Nanoscale dynamics of enhancer'promoter interactions during exit from pluripotency

Gabriela Stumberger and others

Dual mechanism of autophagy gene repression by PHF23 and therapeutic potential of its inhibition in protein aggregation disorders

Seon Ah Choi and others

PKL mediates H3K4me2 modification and spatial gene congregation in chromatin regulation

Mengfei Song and others

Phosphorylation of HP1/Swi6 relieves competition with Suv39/Clr4 on nucleosomes and enables H3K9 trimethyl spreading

Dana R Kennedy and others

METTL3 and METTL14 determine human neural fate specifications

Yanqi Zhang and others

Hangover regulates gene expression by limiting NSL-mediated H4K16 acetylation

Jonathan Lenz and others

Nascent RNA profiling reveals genome-wide productive reiterative initiation regulating gene transcription in bacteria

Zhe Sun and others

RG motifs promote piRNA-mediated gene silencing in C. elegans

Dylan C Wallis and Carolyn M Phillips

Stage-dependent dual mechanisms of MORC2 in retrotransposon silencing and sex chromosome inactivation in germ cells

Zhenlong Kang and others

Systematic enhancer mapping and functional analysis in zebrafish with optimized CRISPR interference

Jiulin Chan and others

Chromatin remodeler ISW-1 orchestrates chromosome axis assembly and meiotic progression in C. elegans

Ruoxi Wang and others

Heterochromatome wide analyses reveal MBD2 as a phase separation scaffold for heterochromatin compartmentalization and composition

Hui Zhang and others

A 5²-UTR cis-acting RNA element targeted by RNase III is essential for DNA simple sequence repeat-dependent phase variation in Haemophilus influenzae

Beatriz RapÃºn-Araiz and others

CDK7'CDK11 axis in spliceosome regulation and pre-mRNA splicing

Michal RÃ¡jeckÃ½ and others

Evolutionary hotspots of structural variation drive inter-individual differences in the expression of fusion transcripts in the human brain

Colette Moses and others

An RBPMS-driven splicing regulatory axis including MBNL1, RBFOX2, and QK promotes smooth muscle cell contractile identity

Yuling Huang and others

3D enhancer architecture coordinated by CTCF determines immune-related gene expression patterns via RNA polymerase II pause-release in CD4⁺ T cells

Eun-Chong Lee and others

PexR is a noncanonical regulator of the peroxide stress response in bacteria

Eva Bastida-MartÃnez and others

Genome Integrity, Repair and Replication

Mlh1'Pms1 couples ATP-driven DNA compaction with nick-dependent endonuclease activation

Bryce W Collingwood and others

Mechanistic insights into the monotherapy and combination potential of FEN1 inhibition in cancer therapy

Eeson Rajendra and others

Telomeric DNA damage landscapes distinguish oxidative from inflammatory cellular stress

Aaron M Fleming and Cynthia J Burrows

Dynamic genome-wide mapping reveals how chromatin context shapes OGG1-mediated repair and related mutagenesis in human cells

Jie Li and others

A nucleoskeleton network preserves genomic integrity by promoting NHEJ and restraining chromosome translocations

Jingyan Liu and others

Pathways and products of base excision DNA repair in Xenopus laevis eggs: contrast with human cell pathways

Zhouyiyuan Xue and others

Processing of DNA single-strand breaks with oxidatively damaged ends by LIG1

Kanal E Balu and others

PARP1 and PARylation facilitate transcription-coupled DNA repair by stabilizing the CSB'RNAPII complex

Mihaela Robu and others

Evidence for a functional interaction between yeast Pol epsilon and PCNA in vivo

Noopur Singh and others

DNA extrusion size determines pathway choice during CAG repeat expansion

Mayuri Bhatia and others

Mutual, spatially limited control of meiotic DNA break formation by Mre11'Rad50'Nbs1 DNA repair complex and Tel1 (ATM) protein kinase

Randy W Hyppa and Gerald R Smith

Genetic evidence for PARP1 trapping as a driver of PARP inhibitor efficacy in BRCA mutant cancer cells

Jonathan Ribeiro and others

A mitotic bookmark coordinates transcription and replication in Drosophila embryos

Chun-Yi Cho and Patrick H O'Farrell

Genomics

De novo origin of numerous microproteins in enterobacteria

Igor Fesenko and others

Molecular and Structural Biology

Distinct quaternary states, intermediates, and autoinhibition during loading of the DnaB-replicative helicase by the phage lambda P helicase loader

Abhipsa Shatarupa and others

Selective elimination of donor bacteria enables global profiling of plasmid gene expression at early stages of conjugation

Meng Wen and others

The yxiD gene from Bacillus subtilis 6633 encodes a polymorphic toxin with tRNase activity and is neutralized by the cognate immunity protein YxxD

Rishita Rohilla and others

Expanding the CarD interaction network: CrsL is a novel transcription regulator in actinobacteria

Mahmoud Shoman and others

Revealing hidden protonated conformational states in RNA dynamic ensembles

Ainan Geng and others

CARF-HAD phosphatase effectors provide immunity during the type III-A CRISPR'Cas response

Gianna Stella and others

Molecular basis of NFIB-mediated regulation of oncogenic transcription

Ci Zhu and others

Structural insights into the exchange mechanism of a replicative DNA polymerase

Xiang Feng and others

The BRD4-nucleosome interaction is enhanced modestly and non-selectively by histone acetylation

Lucien S Lambrechts and others

Acoustically seeded fabrication of a DNA tesseract into a conductive wire

Simon Chi-Chin Shiu and others

Nucleic Acid Enzymes

Loop-mediated regulation and base flipping drive RNA cleavage by human mitochondrial PNPase

Ole Unseld and others

Beyond RNA modification: a novel role for tRNA modifying enzyme in oxidative stress response and metabolism

Louna Fruchard and others

Substrate-induced remodeling of protein disordered loops activates Csm DNases

Zhenxiao Yu and others

Tatdn2 is required for DNA repair to safeguard genome stability in primordial germ cells

Hanqiao Shang and others

A new role for PHYHD1 and related dioxygenases: demethylation of 2²-O-methylated nucleosides

Justas Stonkus and others

Functional analyses of bacterial NanoRNase B proteins reveals defining features of this enzyme family

Tanner M Myers and others

Characterization and engineering of a type IV-A3 CRISPR'Cas system for genome editing in Escherichia coli

Szabolcs Semsey and others

Casdelta , an evolutionary transitional CRISPR system enables efficient genome editing across animals and plants

Zhijia Yang and others

Nucleic Acid Therapeutics

An SpC editor targeting pre-mRNA splicing for precise CRISPR control and enhanced antitumor efficacy

Xiaorui Shi and others

Potent and durable gene modulation in heart and muscle with chemically defined lipophilic siRNAs

Hassan H Fakih and others

RNA and RNA-protein complexes

Comprehensive analysis of yeast +1 ribosomal frameshifting unveils a novel stimulator supporting two distinct frameshifting mechanisms

Darren A Fenton and others

eIF2D promotes 40S ribosomal subunit recycling during intrinsic ribosome destabilization

Kazuya Ichihara and others

RNA'RNA interactome approaches provide in vivo evidence for a critical role of the Hfq rim face in sRNA'mRNA pairing

Xing Luo and others

Genome-wide modulation of alternative splicing by a predicted alpha helix in U2AF2

Dingwu Xue and others

KHNYN is a manganese-dependent endoribonuclease required for ZAP-mediated antiviral restriction

Rebecca L Youle and others

Nucleolar MED19 regulates 2²-O-methylation of rRNA in supporting cancer cell growth

Yang Ming and others

Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT

Hoda Kooshapour and others

Pseudouridine increases ribosome stability in a thermophilic eukaryote

Klemens Wild and others

3²UTR-derived small RNA couples acid resistance to metabolic reprogramming of Salmonella within macrophages

Takeshi Kanda and others

Fernando M GarcÃa-RodrÃguez and others

Synthetic Biology and Bioengineering

Generating functional plasmid origins with OriGen

Jamie Irvine and others

RECODE: a programmable guide-free C-to-U RNA editing tool

Mizuho Ichinose and others

Designing modular genetic sensors with TtgR/AcrR family transcriptional regulators by using a statistical and data-driven approach

Anjita Budhathoki and others

Design of orthogonal and portable RNA devices for post-transcriptional regulation by reverse engineering type I toxin-antitoxin systems

Guobin Yin and others

HyperdCas12a-based multiplexed genetic regulation in Candida albicans

Nicholas C Gervais and others

Methods

Capturing sequence ambiguity among taxa in a primer-specific manner to improve taxonomic classification of amplicon sequencing

Jacob T Nearing and others

CelLink: integrating single-cell multi-omics data with weak feature linkage and imbalanced cell populations

Xin Luo and others

A split luciferase biosensing platform for detection and imaging of chromatin loops in individual live cells

Nicholas G Heath and others

Dividing out quantification uncertainty enables assessment of differential transcript usage with limma and edgeR

Pedro L Baldoni and others

Gene-sized DNA insertion at genomic safe harbors in human cells using a site-directed transposase

James E Short and others

A spatially informed matrix normal model for gene co-expression analysis in spatial transcriptomics studies

Chichun Tan and Ying Ma

ConSeqUMI, an error-free nanopore sequencing pipeline to identify and extract individual nucleic acid molecules from heterogeneous samples

Adam M Zahm and others

DENetwork unveils non-differentially expressed genes with functional relevance across conditions through information flow perturbation

Bowen Zhao and others

codonGPT: reinforcement learning on a generative language model enables scalable mRNA design

Binita Rajbanshi and Anuj Guruacharya

InCURA: integrative gene clustering based on transcription factor binding sites

Lorna Rinck and others

Structure-informed models for ionic current prediction in nanopore sequencing of expanded dna alphabets

Ashley Stephenson and others

A novel plasmid-based co-tethered transcription platform for high yield, high purity mRNA synthesis

Purnima Mala and others

Quantifying transcription factor specificity with advanced DNA universal microarrays featuring long and modified binding sites

Yuval Bayer and others

Detecting signatures underlying the composition of biological data

Anthony Duncan and others

Corrections

Correction to ˜mRNA turnover dynamics are affected by cell differentiation and loss of the cytosine methyltransferase Nsun2'

Editor's Note

Editor's Note on ˜A bi-functional siRNA construct induces RNA interference and also primes PCR amplification for its own quantification'

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