Subject: New issue: Nucleic Acids Research, Volume 54, Issue 1, 13 January 2026

Volume 54, Issue 1, 13 January 2026

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Critical Reviews and Perspectives

Unravelling the noncanonical extracellular DNA structures in biofilm and NETosis

Tevriz Dilan Demir and others

Chemical Biology and Nucleic Acid Chemistry

Directed evolution on compact landing pads yields highly efficient recombinases for large DNA integration

Hanseop Kim and others

Allele-specific knockdown by an engineered DNAzyme capable of RNase H1 evasion

Erica M Lee and others

A universal kinetic framework for quantitative isothermal amplification governed by polymerase speed, amplicon size, and binding efficiency

Langjun Tang and others

Specificity of the stabilizing interaction between intrinsically disordered protein sequences and G-quadruplexes in RNA

Lachlan B Cox and others

Junction-targeting designs limit the application of CRISPR-Cas13d in circular RNA perturbation studies

Yannick C Lee-yow and others

Recognition of unnatural base pairs by a eukaryotic DNA polymerase enables universal sequencing of an expanded genetic alphabet

Hantao Luo and others

Presence of phosphodiester backbone, but not nucleobases, in the guide's 3² terminal region is necessary for RISC loading and target cleavage in vitro and in vivo

Daniel O'Reilly and others

Computational Biology

Uncovering coordinated pathway interactions through gene co-differential expression in yeast

Muhammad Ibtisam Nasar and others

A structure-guided approach to noncoding variant evaluation for transcription factor binding using AlphaFold 3

Lukas Gerasimavicius and others

scSuperAnnotator: a platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data

Qi Qi and others

A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen

Cristobal Carrera Carriel and others

Data Resources and Analyses

Protein structure-informed bacteriophage genome annotation with Phold

George Bouras and others

DNATCO v5.0: integrated web platform for 3D nucleic acid structure analysis

JiÅ™Ã Ä'ernÃ½ and others

Gene Regulation, Chromatin and Epigenetics

No evidence for the putative nitric oxide sensor NsrR as a key regulator of magnetosome formation in Magnetospirillum gryphiswaldense

Alexandra Woller and others

Systemic control of HNF1B-driven redox homeostasis by N⁶-adenosine methylation

Minji Park and others

Facultative heterochromatin mediated by core and accessory chromosome-encoded H3K27-specific methyltransferases controls virulence in a fungal phytopathogen

Slavica Janevska and others

Phosphorylation-dependent modulation of the Lamin A/C'EZH2 complex regulates epithelial'mesenchymal plasticity

Balaji AK and others

YAP-TEAD regulates the super-enhancer network to control early surface ectoderm commitment

Zhiming Wang and others

A conserved 3²UTR short motif regulates gene expression in vertebrates

Ana EufrÃ¡sio and others

RNA polymerase II degradation triggered by DNA repair occurs in trans and independently of how the lesion is recognized

Ramveer Choudhary and others

Activation of bacterial transcription by distortion of promoter base pairing

Ksenia M Klimova and others

Effector gene silencing coordinated by histone methylation and small RNAs enhances host adaptation in a plant pathogen

Liyuan Wang and others

Sequence-dependent co-condensation of Lsr2 with DNA elucidates the mechanism of genome compaction in Mycobacterium tuberculosis

Prakshi Gaur and others

Co-transcriptional splicing changes combine with reduced productive transcription initiation for cold-induced repression of FLC

Robert Maple and others

Dual transcriptional and post-transcriptional regulation by the bHLH proteins Rtg1 and RtgX in Komagataella phaffii

Neetu Rajak and others

Linker histone H1.5 contributes to centromere integrity

Ankita Saha and others

HLTF cooperates with GATA1 to activate transcriptional programs and chromatin remodeling during erythroid development

Han Gong and others

Genome Integrity, Repair and Replication

PARP1 and PARP2 are dispensable for DNA repair by microhomology-mediated end-joining at double-ended DSBs

Raquel Ortega and others

PCNA encircling primer/template junctions is eliminated by exchange of RPA for Rad51: implications for the interplay between human DNA damage tolerance pathways

Jessica L Norris and others

A mechanism for telomere-specific telomere length regulation

Gabriela M Teplitz and others

Transcriptional PBR cycles at pericentromeric repeats cause gross chromosomal rearrangements through Rad52-dependent ADR-loop formation

Ran Xu and others

Genomics

Replication stress increases de novo CNVs across the malaria parasite genome

Noah Brown and others

Molecular and Structural Biology

Sequential structural rearrangements at the PAM-distal site of a type I-F3 CRISPR-Cas effector enabling RNA-guided DNA transposition

Kazuki Ishihara and others

Beyond DNA binding: single C2H2 zinc fingers with adjacent beta -strands mediate dimerization in Drosophila transcription factors

Konstantin I Balagurov and others

An N-terminal helix of Lsm11 stabilizes CPSF73 in U7 snRNP for histone pre-mRNA 3²-end processing

Anthony Desotell and others

Structural evolution of the selectivity clamp confers ADPR-PP specificity in Namat, a phage nicotinamide ADP-ribose transferase

Meimei Lan and others

Multimodal bHLH-PAS DNA binding controls specificity and drives obesity

David C Bersten and others

New targets and procedures for validating the valence geometry of nucleic acid structures

JiÅ™Ã Ä'ernÃ½ and others

Eukaryotic initiation factor eIF3 facilitates loading of eukaryotic release factor eRF1 or suppressor tRNA to the ribosome

Ekaterina Shuvalova and others

Structural insights into Ïƒ²⁸-dependent transcription initiation and its regulation by anti-sigma factor in Pseudomonas aeruginosa

Sheenu and others

Structure of Bacillus subtilis Ku-mediated DNA synaptic complex

Whan-Jong Kim and others

Bringing the ends together: cryo-EM structures of mycobacterial Ku in complex with DNA define its role in NHEJ synapsis

Joydeep Baral and others

Foliar-applied double-stranded RNA is mobile, transfers to plant pathogens, and triggers RNAi

Christopher A Brosnan and others

Nucleic Acid Enzymes

Structure and function of the RNA polymerase complex of Borna disease virus, a nuclear-replicating non-segmented negative-strand RNA virus

Eric Gibbs and others

Modular determinants of cleavage preference in GIY-YIG nucleases revealed by block-based DNA shuffling and directed evolution

Kurt W Loedige and others

The DinG exonuclease acts as a primary quality controller to remove unprocessed ribosomal RNAs

Karolis VaitkeviÄius and JÃ¶rgen Johansson

A modified X10-23 DNAzyme that can better access large, structured RNA targets

Connor Nurmi and others

Enhanced SfaTnpB enables single-base-specific, one-pot nucleic acid detection for high-sensitivity diagnostics

Bingrong Xu and others

Differential association of primary and alternative Ïƒ factors with RNA polymerase of Mycobacterium tuberculosis during transcription elongation

Nilanjana Hazra and Jayanta Mukhopadhyay

Nuc domain electrostatics drive the trans cleavage activity of CRISPR'Cas12a

Anthony Newman and others

Nucleic Acid Therapeutics

Argonaute-mediated RNA editing selectively repairs point mutations

Zhiwei Zhang and others

RNA and RNA-protein complexes

Division of labor in trypanosome RNA processing and export through expanded Mex67 paralogs

Samson O Obado and others

ERK phosphorylates HNRNPF to promote the proliferation and suppress the differentiation of embryonic stem cells

Xiaowei Duan and others

Crystal structures of Caenorhabditis elegans PUF-3 depict plasticity of RNA recognition that enables germline gene regulation

Yingying Zhang and others

Mechanistic insights into Lin28-dependent oligo-uridylylation of pre-let-7 by TUT4

Xiaojie Han and others

Potyviruses recruit host eIF4A3 to block m⁶A-mediated RNA decay by steric hindrance of viral RNA methylation in plants

Dezhi Peng and others

Binding of Glycyl-tRNA synthetase to Mengovirus RNA stimulates translation

Fabian DroÃŸ and others

Initial spliceosomal U4/U6 di-snRNA formation occurs in the cytoplasm of Saccharomyces cerevisiae and requires a guard protein mediated quality control

Xiaoxiao Wang and others

Maternal TDP43 orchestrates nuclear speckle assembly and zygotic splicing activation during oocyte-to-embryo transition in mice

Zuo-Qi Deng and others

Synthetic Biology and Bioengineering

Specific killing and resensitization of pathogenic Escherichia coli strains carrying bla_CTX-M-15 beta -lactamase using targeted-antibacterial-plasmids (TAPs)

Elisabeth Derollez and others

Triplex DNA clamp regulates Cas12a activation for ssDNA and RNA sensing

Andrea Celeste Di Pede and others

A unified computational framework for quantitative design and optimization of transcriptional regulation across bacterial species

Tianze Wang and others

Design of bacterial DNT sensors based on computational models

Shir Bahiri Elitzur and others

Methods

SCALE: unsupervised multiscale domain identification in spatial omics data

Behnam Yousefi and others

Single-molecule mechanostructural fingerprinting of nucleic acid conformations

Prakash Shrestha and others

The nuclear cap-binding complex regulates subcellular RNA processing and surveillance of coding and noncoding RNAs

Diep R Ganguly and Brian D Gregory

Microenvironment-aware spatial modeling for accurate inference of cell identity

Qi Liu and others

Accurate detection of somatic single-nucleotide variants from bulk RNA-seq data using RNA-MosaicHunter

August Yue Huang and others

STAN, a computational framework for inferring spatially informed transcription factor activity

Linan Zhang and others

CellMap: precision mapping of cellular landscape in spatial transcriptomics

Hongjia Liu and others

SVCROWS: a user-defined tool for interpreting significant structural variants in heterogeneous datasets

Noah Brown and others

Accurate chromatin marks peak calling with Omnipeak

Oleg Shpynov and Maxim N Artyomov

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