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 König 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 Rapún-Araiz and others
CDK7'CDK11 axis in spliceosome regulation and pre-mRNA splicing
Michal Rájecký 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
Structurally related phage helicases trigger type III-A3 retron-mediated anti-phage defense across diverse tailed phage families
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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