Subject: New issue: Nucleic Acids Research, Volume 53, Issue 17, 23 September 2025

Volume 53, Issue 17, 23 September 2025

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Control of the archaeal DNA damage-responsive pathway by phosphorylation of Orc1-2, the global regulator in Saccharolobus islandicus

Xiaotong Liu and others

NAR Breakthrough Article

Visualizing intracellular glycine with two-dye and single-dye ratiometric RNA-based sensors

Madeline R Bodin and Ming C Hammond

Critical Reviews and Perspectives

Harnessing the potential of spatial statistics for spatial omics data with pasta

Martin Emons and others

Chemical Biology and Nucleic Acid Chemistry

Molecular recognition and effects of a benzothiazole derivative targeting the MYC G-quadruplex

Xiao Ni and others

Computational Biology

Investigating the performance of foundation models on human 3²UTR sequences

Sergey Vilov and Matthias Heinig

Cancer histone mutations impact protein binding and DNA repair with possible links to genomic instability

Daniel Espiritu and others

Gene Regulation, Chromatin and Epigenetics

SMRT anchors the HDAC3 corepressor complex to chromatin to regulate inflammatory and metabolic pathways in macrophages

Astradeni Efthymiadou and others

CRISPR-Cas9 targeting of G-Quadruplex DNA in ADH1 promoter highlights its role in transcriptome and metabolome regulation

Ikenna Obi and others

Phosphorylation of H3.3 at Serine 31 acts as a switch of nucleosome dynamics for transcription

Jingzhe Ma and others

Lactylation of CREB is required for FSH-induced proliferation and differentiation of ovarian granulosa cells

Gang Wu and others

The nuclear pore complex acts as a hub for pri-miRNA transcription and processing in plants

Lucia Gonzalo and others

INO80/SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape

Meitong Liu and others

Post-translational modification of H2B C-terminal helix regulates nucleosome interactions and chromatin signaling

Yani Zhao and others

Translesion DNA polymerases Rev1 and PolH promote LTR-retrotransposon transcription by safeguarding Pol II occupancy in both germline and somatic tissues of Drosophila

Chongyang Li and others

Genome Integrity, Repair and Replication

UVA-induced DNA damage and mutations in human melanocytes: relevance for melanoma mutations

Seung-Gi Jin and others

Exclusion systems preserve host cell homeostasis and fitness, ensuring successful dissemination of conjugative plasmids and associated resistance genes

Agathe Couturier and others

Profiling BRCA1-BRCT interactions and their functional relevance at amino acid resolution

Venda Mangkusaputra and others

Translesion polymerases and DNA'protein crosslink repair shapes the cellular response to formaldehyde-induced DNA damage in ssDNA

Thomas Blouin and others

Molecular and Structural Biology

Autophosphorylation of conserved yeast and human casein kinase 1 isozymes regulates Elongator-dependent tRNA modifications

Maria Friederike Landrock and others

Crystal structures of distinct parallel and antiparallel DNA G-quadruplexes reveal structural polymorphism in C9orf72 G4C2 repeats

Yanyan Geng and others

Structural basis of bis-quinolinium ligands binding to quadruplex'duplex hybrids from PIM1 oncogene

Anirban Ghosh and others

Promoter-proximal transcription'translation coupling controls early transcription in Escherichia coli

Soojin Park and others

Mutations on the surface of HDAC1 reveal molecular determinants of specific complex assembly and their requirement for gene regulation

Ahmad Alshehri and others

Naphthyridine carbamate dimer ligand induces formation of Z-RNA-like fold of disease-related RNA and exhibits a molecular glue characteristics in crystal lattice formation

Martyna Mateja-Pluta and others

Decoding the base flipping mechanism of the SET- and RING-associated (SRA) domain of the epigenetic UHRF1 protein

Dipanjan Mukherjee and others

Nucleic Acid Enzymes

Deciphering the dark side of histone ADP-ribosylation: what structural features of damaged nucleosome regulate the activities of PARP1 and PARP2

Tatyana A Kurgina and others

CRISPR/Cas12a DTR system: a topology-guided Cas12a assay for specific dual detection of RNA and DNA targets

Qingyuan Jiang and others

The displacement of the Ïƒ⁷⁰ finger in initial transcription is highly heterogeneous and promoter-dependent

Anna Wang and others

OLD amputates the anticodon arm of tRNAs during P2'Lambda interference

Apurva A Govande and others

Structural mechanism of RECQ1 helicase in unfolding G-quadruplexes compared with duplex DNA

Ze-Yu Song and others

AsCas12a tolerates insertions in target DNA

Santosh R Rananaware and others

RNA and RNA-protein complexes

Molecular basis for the recognition of low-frequency polyadenylation signals by mPSF

Lin Huang and others

Ligand specificity and adaptability revealed by the first Guanine-II riboswitch tertiary structure

Hongcheng Li and others

Synthetic Biology and Bioengineering

Integrating recombinase-based feedback and feedforward control for optimal resource decoupling

Rixin Zhang and others

In vivo pathway optimization in yeast via loxpsym-mediated shuffling of upstream activating sequences

Ciaran Ruehmkorff and others

Methods

EASY-edit: a toolbox for high-throughput single-step custom genetic editing in bacteria

Maxence Lejars and others

Synthesizing supercoiled circular DNA molecules in vitro

Sepideh Rezaei and others

WarpDemuX-tRNA: barcode multiplexing for nanopore tRNA sequencing

Wiep van der Toorn and others

A NanoLock-enabled, Craspase-based strategy for highly sensitive RNA detection

Yumeng Xiao and others

Toward standardized epitranscriptome analytics: an inter-laboratory comparison of mass spectrometric detection and quantification of modified ribonucleosides in human RNA

Martin Hengesbach and others

A simple, fast, and cost-efficient protocol for ultra-sensitive ribosome profiling

JiÅ™Ã Koubek and others

Enspyre: a novel enrichment technology for selected DNA variants using pyrophosphorolysis

Katarzyna A Anton and others

Label-free technique for universal and sequence independent detection of oligonucleotides and nuclease activity

Negin Gooran and others

Corrections

Correction to ˜RIG-I recognizes metabolite-capped RNAs as signaling ligands'

Correction to ˜Structure of the nucleosome-bound human BCL7A'

Editor's Note

Editor's Note on ˜Inhibition of cyclin D1 expression by androgen receptor in breast cancer cells'identification of a novel androgen response element'

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