Subject: New issue: Nucleic Acids Research, Volume 53, Issue 15, 28 August 2025

Volume 53, Issue 15, 28 August 2025

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Matters Arising

Response to "Antiviral RNA silencing in mammals: the importance of selecting the appropriate experimental model"

Petr Svoboda and Radek Malik

Antiviral RNA silencing in mammals: the importance of selecting the appropriate experimental model

Xing Liu and Yang Li

NAR Breakthrough Article

Promoter-targeted small RNA duplexes increase MBNL1 transcription and mitigate myotonic dystrophy-associated spliceopathy

Nikola MusiaÅ‚a-Kierklo and others

Critical Reviews and Perspectives

Mechanisms underlying low mutation rates in mammalian oocytes and preimplantation embryos

Nataliia Dudko and others

Chemical Biology and Nucleic Acid Chemistry

Hemin-binding DNA structures on the surface of bacteria promote extracellular electron transfer

Obinna M Ajunwa and others

Computational Biology

Peripheral heterochromatin tethering is required for chromatin-based nuclear mechanical response

Ali GÃ¶ktuÄŸ Attar and others

Data Resources and Analyses

MoDorado: enhanced detection of tRNA modifications in nanopore sequencing by off-label use of modification callers

Franziskus N M RÃ¼bsam and others

Gene Regulation, Chromatin and Epigenetics

Translocations can drive expression changes of multiple genes in regulons covering entire chromosome arms

Anna Oncins and others

Comprehensive mapping of transcription terminator Rho utilization (Rut) sites across the Bacillus subtilis genome

Mildred Delaleau and others

The p400 complex promotes HIV-1 latency by suppressing viral transcription and altering the host cell state

Luisa P Mori and others

Orchestrated long-distance gene activation by a ParB-like BisD-CTP DNA clamp in low-frequency transfer competence development in Pseudomonas putida

Hammam Antar and others

Ints7 deficiency activates DNA damage response to elicit resurgence of endogenous retrovirus MERVL and anastasis of embryonic stem cells

Yunfan Shen and others

Systematic modulation of bacterial resource allocation by perturbing RNA polymerase availability via synthetic transcriptional switches

Manlu Zhu and Xiongfeng Dai

Genome Integrity, Repair and Replication

The Influence of CG sites on dynamic DNA sequence mutagenesis in the genomic evolution of mammalian lifespan

Steven S Smith

Distinct mechanisms underlying extrachromosomal telomere DNA generation in ALT cancers

Junyeop Lee and others

Replication program of a single-chromosome budding yeast strain

Jade Pellet and others

The human primosome requires replication protein A when copying DNA with inverted repeats

Andrey G Baranovskiy and others

Molecular and Structural Biology

Deciphering the RNA recognition by Musashi-1 to design protein and RNA variants for in vitro and in vivo applications

Anna PÃ©rez-RÃ fols and others

A common structural mechanism for RNA recognition by the SF3B complex in mRNA splicing and export

Yuzhu Zhang and others

PAM-interacting domain turn-helix 51 motifs can improve Cas9'SpRY activity

Reto Eggenschwiler and others

Internal ribosome entry sites enhance translation in trans in antisense non-coding SINEUP and circular RNAs

Sabrina D'Agostino and others

DHX8 regulates degradation of RNA by RNautophagy

Ryohei Sakai and others

Nucleic Acid Enzymes

RECQ5 mediates pre-rRNA processing in nucleolus

Yidi Ma and Xiaochun Yu

Fidelity, specialization, and evolution of Paramecium PolX DNA polymerases involved in programmed double-strand break DNA repair

Nourisson Antonin and others

Nucleic Acid Therapeutics

Gene editing in hematopoietic stem cells by co-delivery of Cas9/sgRNA ribonucleoprotein and templates for homology-directed repair in ˜all-in-one' lentivirus-derived nanoparticles

Sofie Andersen and others

SLFN11-mediated tRNA regulation induces cell death by disrupting proteostasis in response to DNA-damaging agents

Yuki Iimori and others

RNA and RNA-protein complexes

Structure-based insights into the ligand specificity tuning of 2²-dG-III riboswitch

Xin Shen and others

Presence of group II introns in phage genomes

Liana N Merk and others

MALAT1 regulates mRNA processing through sequence dependent RNA'RNA and RNA'protein interactions

Adarsh Balaji and others

Plant mitochondrial PORR proteins facilitate group II intron splicing by binding to distinct regions within their target introns

Chuande Wang and others

A time-resolved framework for the recruitment of mRNP processing and assembly factors to a site of transcription

Theresa Wechsler and others

Sm-site containing mRNAs can accept Sm-rings and are downregulated in Spinal Muscular Atrophy

Anton J Blatnik, III and others

The kinase GSK-3 alters the RNA-binding protein landscape of lipid metabolism transcripts leading to altered expression in the C. elegans nervous system

Ananya Mahapatra and others

Synthetic Biology and Bioengineering

A rapid and efficient red-light-activated Cre recombinase system for genome engineering in mammalian cells and transgenic mice

Yang Zhou and others

Adaptive evolution of oriC through in vitro propagation of a mini-chromosome in RCR

Shota Suzuki and Masayuki Su'etsugu

Dual-mode CRISPRa/i for genome-scale metabolic rewiring in Escherichia coli

Soo Young Moon and others

Methods

Engineering of high-precision C-to-G base editors with expanded site selectivity and target compatibility

Zheng Li and others

Cell sorting based on single nucleotide variation enables characterization of mutation-dependent transcriptome and chromatin states

Roberto Salatino and others

PIRT-Seq: a high-resolution whole-genome assay to identify protein-coding genes

Emily C A Goodall and others

Oncodrive3D: fast and accurate detection of structural clusters of somatic mutations under positive selection

Stefano Pellegrini and others

Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid'protein interaction sites by mass spectrometry

Luisa M Welp and others

Tier-based standards for FAIR sequence data and metadata sharing in microbiome research

Lina Kim and others

ONE-STEP tagging: a versatile method for rapid site-specific integration by simultaneous reagent delivery

Valentina Migliori and others

Genome-wide in vivo and ex vivo mapping of R-loops using engineered N-terminal hybrid-binding domain of RNase H3 (enDR3)

Marta Jedynak-Slyvka and others

Kingdom-wide CRISPR guide design with ALLEGRO

Amirsadra Mohseni and others

Inferring causal trajectories from spatial transcriptomics using CASCAT

Yingying Yu and others

ECSFinder: optimized prediction of evolutionarily conserved RNA secondary structures from genome sequences

Vanda Gaonac'h-Lovejoy and others

Corrections

Correction to ˜A high-throughput single-molecule platform to study DNA supercoiling effect on protein'DNA interactions'

Expression of Concern

Expression of Concern on ˜Human base excision repair complex is physically associated to DNA replication and cell cycle regulatory proteins'

Expression of Concern on ˜NicOPURE: nickless RNA circularization and one-step purification with engineered group II introns and cyclizing UTRs'

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