Volume 52, Issue 18
14 October 2024
Cover image
Cover image
Cover: Artwork from the project Visual Arts for Science in Argentina. Drawing by Oscar Ortiz and Andrea Gamarnik. The image portrays an artistic representation of the 3D structure of a small subgenomic RNA generated during Zika virus infection. This RNA, known as sfRNA, participates in a novel mechanism that arrests cellular translation to counteract the human cell's antiviral response.
For more information see article by Pallarés, H.M. et al., pages 11128–11147 in this issue.
For more information see article by Pallarés, H.M. et al., pages 11128–11147 in this issue.
ISSN 0305-1048
EISSN 1362-4962
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Volume 52, Issue 18, 14 October 2024
NAR Breakthrough Article
Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein–protein interactions
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10731–10746, https://doi.org/10.1093/nar/gkae692
Critical Reviews and Perspectives
Striving for clarity in language about gene expression
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10747–10753, https://doi.org/10.1093/nar/gkae764
Chemical Biology and Nucleic Acid Chemistry
Synthesis of 2′-formamidonucleoside phosphoramidites for suppressing the seed-based off-target effects of siRNAs
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10754–10774, https://doi.org/10.1093/nar/gkae741
Modulation of dynamic DNA G-quadruplex structures in the hTERT promoter region by ligands
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10775–10787, https://doi.org/10.1093/nar/gkae754
Trinucleotide cap analogs with triphosphate chain modifications: synthesis, properties, and evaluation as mRNA capping reagents
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10788–10809, https://doi.org/10.1093/nar/gkae763
Identification of an RNA-binding perturbing characteristic for thiopurine drugs and their derivatives to disrupt CELF1–RNA interaction
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10810–10822, https://doi.org/10.1093/nar/gkae788
Computational Biology
Unlocking precision in aptamer engineering: a case study of the thrombin binding aptamer illustrates why modification size, quantity, and position matter
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10823–10835, https://doi.org/10.1093/nar/gkae729
Machine learning unravels inherent structural patterns in Escherichia coli Hi-C matrices and predicts chromosome dynamics
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10836–10849, https://doi.org/10.1093/nar/gkae749
ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10850–10861, https://doi.org/10.1093/nar/gkae758
SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10862–10878, https://doi.org/10.1093/nar/gkae772
Gene Regulation, Chromatin and Epigenetics
ALKBH5 governs human endoderm fate by regulating the DKK1/4-mediated Wnt/β-catenin activation
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10879–10896, https://doi.org/10.1093/nar/gkae707
Unexpected nuclear hormone receptor and chromatin dynamics regulate estrous cycle dependent gene expression
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10897–10917, https://doi.org/10.1093/nar/gkae714
Heterochromatin protein 1 alpha (HP1α) undergoes a monomer to dimer transition that opens and compacts live cell genome architecture
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10918–10933, https://doi.org/10.1093/nar/gkae720
The impact of the embryonic DNA methylation program on CTCF-mediated genome regulation
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10934–10950, https://doi.org/10.1093/nar/gkae724
DipR, a GntR/FadR-family transcriptional repressor: regulatory mechanism and widespread distribution of the dip cluster for dipicolinic acid catabolism in bacteria
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10951–10964, https://doi.org/10.1093/nar/gkae728
Genome Integrity, Repair and Replication
Loss of DNA glycosylases improves health and cognitive function in a C. elegans model of human tauopathy
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10965–10985, https://doi.org/10.1093/nar/gkae705
Dispensability of HPF1 for cellular removal of DNA single-strand breaks
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10986–10998, https://doi.org/10.1093/nar/gkae708
Replication fork stalling in late S-phase elicits nascent strand degradation by DNA mismatch repair
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 10999–11013, https://doi.org/10.1093/nar/gkae721
Second generation lethality in RNAseH2a knockout zebrafish
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11014–11028, https://doi.org/10.1093/nar/gkae725
Mechanism of structure-specific DNA binding by the FANCM branchpoint translocase
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11029–11044, https://doi.org/10.1093/nar/gkae727
Genomics
Long range segmentation of prokaryotic genomes by gene age and functionality
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11045–11059, https://doi.org/10.1093/nar/gkae745
Molecular and Structural Biology
HIV-1 usurps mixed-charge domain-dependent CPSF6 phase separation for higher-order capsid binding, nuclear entry and viral DNA integration
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11060–11082, https://doi.org/10.1093/nar/gkae769
Structural insights into the biosynthetic mechanism of Nα-GlyT and 5-NmdU hypermodifications of DNA
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11083–11097, https://doi.org/10.1093/nar/gkae784
How to scan naked DNA using promiscuous recognition and no clamping: a model for pioneer transcription factors
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11098–11114, https://doi.org/10.1093/nar/gkae790
Crystal structure and nucleic acid binding mode of CPV NSP9: implications for viroplasm in Reovirales
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11115–11127, https://doi.org/10.1093/nar/gkae803
Molecular Biology
Zika virus non-coding RNAs antagonize antiviral responses by PKR-mediated translational arrest
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11128–11147, https://doi.org/10.1093/nar/gkae507
Nucleic Acid Enzymes
Synergistic effect of split DNA activators of Cas12a with exon-unwinding and induced targeting effect
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11148–11157, https://doi.org/10.1093/nar/gkae766
RTP801 interacts with the tRNA ligase complex and dysregulates its RNA ligase activity in Alzheimer’s disease
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11158–11176, https://doi.org/10.1093/nar/gkae776
Making target sites in large structured RNAs accessible to RNA-cleaving DNAzymes through hybridization with synthetic DNA oligonucleotides
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11177–11187, https://doi.org/10.1093/nar/gkae778
Accelerated discovery and miniaturization of novel single-stranded cytidine deaminases
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11188–11202, https://doi.org/10.1093/nar/gkae800
RNA and RNA-protein complexes
Complete list of canonical post-transcriptional modifications in the Bacillus subtilis ribosome and their link to RbgA driven large subunit assembly
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11203–11217, https://doi.org/10.1093/nar/gkae626
Structural basis for a highly conserved RNA-mediated enteroviral genome replication
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11218–11233, https://doi.org/10.1093/nar/gkae627
Dynamics of diversified A-to-I editing in Streptococcus pyogenes is governed by changes in mRNA stability
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11234–11253, https://doi.org/10.1093/nar/gkae629
Assembly of the bacterial ribosome with circularly permuted rRNA
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11254–11265, https://doi.org/10.1093/nar/gkae636
LRPPRC and SLIRP synergize to maintain sufficient and orderly mammalian mitochondrial translation
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11266–11282, https://doi.org/10.1093/nar/gkae662
Global analysis of the RNA–RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11283–11300, https://doi.org/10.1093/nar/gkae668
Structural Biology
Structural basis for difunctional mechanism of m-AMSA against African swine fever virus pP1192R
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11301–11316, https://doi.org/10.1093/nar/gkae703
Structural basis of AUC codon discrimination during translation initiation in yeast
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11317–11335, https://doi.org/10.1093/nar/gkae737
Structural basis for the concerted antiphage activity in the SIR2–HerA system
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11336–11348, https://doi.org/10.1093/nar/gkae750
Structural basis of DNA recognition by BEN domain proteins reveals a role for oligomerization in unmethylated DNA selection by BANP
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11349–11361, https://doi.org/10.1093/nar/gkae762
Synthetic Biology and Bioengineering
Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11362–11377, https://doi.org/10.1093/nar/gkae742
CRISETR: an efficient technology for multiplexed refactoring of biosynthetic gene clusters
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11378–11393, https://doi.org/10.1093/nar/gkae781
Reconstruction of a robust bacterial replication module
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11394–11407, https://doi.org/10.1093/nar/gkae786
Correction
Correction to ‘Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch’
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Page 11408, https://doi.org/10.1093/nar/gkae751
Correction to ‘Structural basis for difunctional mechanism of m-AMSA against African swine fever virus pP1192R’
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Page 11409, https://doi.org/10.1093/nar/gkae771
Correction to ‘Efficient circularization of protein-encoding RNAs via a novel cis-splicing system’
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Pages 11410–11411, https://doi.org/10.1093/nar/gkae801
Correction to ‘MRE11 UFMylation promotes ATM activation’
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Page 11412, https://doi.org/10.1093/nar/gkae802
Correction to ‘Advancing quantitative PCR with color cycle multiplex amplification’
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Page 11413, https://doi.org/10.1093/nar/gkae827
Correction to ‘Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria’
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Page 11414, https://doi.org/10.1093/nar/gkae836
Methods
Identification of transcription factor co-binding patterns with non-negative matrix factorization
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Page e85, https://doi.org/10.1093/nar/gkae743
Force-enhanced sensitive and specific detection of DNA-intercalative agents directly from microorganisms at single-molecule level
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Page e86, https://doi.org/10.1093/nar/gkae746
Learning to quantify uncertainty in off-target activity for CRISPR guide RNAs
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Page e87, https://doi.org/10.1093/nar/gkae759
DFF-ChIP: a method to detect and quantify complex interactions between RNA polymerase II, transcription factors, and chromatin
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Page e88, https://doi.org/10.1093/nar/gkae760
DORQ-seq: high-throughput quantification of femtomol tRNA pools by combination of cDNA hybridization and Deep sequencing
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Page e89, https://doi.org/10.1093/nar/gkae765
Using nucleolytic toxins as restriction enzymes enables new RNA applications
Nucleic Acids Research, Volume 52, Issue 18, 14 October 2024, Page e90, https://doi.org/10.1093/nar/gkae779
