Volume 52, Issue 12
8 July 2024
Cover image
Cover image
Cover: Protein–DNA recognition kinetics are characterized by two key elements: the time taken to locate the target site (shown here in blue) amid various nonspecific alternatives (shown in purple); and the kinetics involved in the recognition process, which may necessitate overcoming an energetic barrier associated with kinking of the DNA. The coordination of the timing of finding the target site and its kinking may result in unproductive binding and the protein (shown in yellow) will skip from the site till the next opportunity to bind will be achieved. This picture was drawn by Daniel Philosoph.
For more information see article by Rogoulenko, E. et al., pages 6763–6776 in this issue.
For more information see article by Rogoulenko, E. et al., pages 6763–6776 in this issue.
ISSN 0305-1048
EISSN 1362-4962
Issue navigation
Volume 52, Issue 12, 8 July 2024
Chemical Biology and Nucleic Acid Chemistry
Site-specific regulation of RNA editing with ribose-modified nucleoside analogs in ADAR guide strands
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 6733–6747, https://doi.org/10.1093/nar/gkae461
Unlocking the potential of protein-derived peptides to target G-quadruplex DNA: from recognition to anticancer activity
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 6748–6762, https://doi.org/10.1093/nar/gkae471
Computational Biology
Skipping events impose repeated binding attempts: profound kinetic implications of protein–DNA conformational changes
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 6763–6776, https://doi.org/10.1093/nar/gkae333
Generating, modeling and evaluating a large-scale set of CRISPR/Cas9 off-target sites with bulges
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 6777–6790, https://doi.org/10.1093/nar/gkae428
CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 6791–6801, https://doi.org/10.1093/nar/gkae444
In silico design of DNA sequences for in vivo nucleosome positioning
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 6802–6810, https://doi.org/10.1093/nar/gkae468
Gene Regulation, Chromatin and Epigenetics
CARM1 hypermethylates the NuRD chromatin remodeling complex to promote cell cycle gene expression and breast cancer development
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 6811–6829, https://doi.org/10.1093/nar/gkae329
A-MYB substitutes for B-MYB in activating cell cycle genes and in stimulating proliferation
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 6830–6849, https://doi.org/10.1093/nar/gkae370
Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 6850–6865, https://doi.org/10.1093/nar/gkae372
Protein phosphatase PP1 regulation of RNA polymerase II transcription termination and allelic exclusion of VSG genes in trypanosomes
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 6866–6885, https://doi.org/10.1093/nar/gkae392
New Drosophila promoter-associated architectural protein Mzfp1 interacts with CP190 and is required for housekeeping gene expression and insulator activity
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 6886–6905, https://doi.org/10.1093/nar/gkae393
NF-κB factors cooperate with Su(Hw)/E4F1 to balance Drosophila/human immune responses via modulating dynamic expression of miR-210
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 6906–6927, https://doi.org/10.1093/nar/gkae394
Alternative translation initiation by ribosomal leaky scanning produces multiple isoforms of the Pif1 helicase
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 6928–6944, https://doi.org/10.1093/nar/gkae400
The p21CIP1-CDK4-DREAM axis is a master regulator of genotoxic stress-induced cellular senescence
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 6945–6963, https://doi.org/10.1093/nar/gkae426
Genome Integrity, Repair and Replication
The BRCA2 R2645G variant increases DNA binding and induces hyper-recombination
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 6964–6976, https://doi.org/10.1093/nar/gkad1222
Dysregulated DnaB unwinding induces replisome decoupling and daughter strand gaps that are countered by RecA polymerization
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 6977–6993, https://doi.org/10.1093/nar/gkae435
The loss of DNA polymerase epsilon accessory subunits POLE3–POLE4 leads to BRCA1-independent PARP inhibitor sensitivity
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 6994–7011, https://doi.org/10.1093/nar/gkae439
Concurrent D-loop cleavage by Mus81 and Yen1 yields half-crossover precursors
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7012–7030, https://doi.org/10.1093/nar/gkae453
The translocation activity of Rad54 reduces crossover outcomes during homologous recombination
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7031–7048, https://doi.org/10.1093/nar/gkae474
Genomics
Pseudogenes in plasmid genomes reveal past transitions in plasmid mobility
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7049–7062, https://doi.org/10.1093/nar/gkae430
PHF2 regulates genome topology and DNA replication in neural stem cells via cohesin
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7063–7080, https://doi.org/10.1093/nar/gkae457
Molecular Biology
Maf1 phosphorylation is regulated through the action of prefoldin-like Bud27 on PP4 phosphatase in Saccharomyces cerevisiae
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7081–7095, https://doi.org/10.1093/nar/gkae414
Primordial aminoacyl-tRNA synthetases preferred minihelices to full-length tRNA
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7096–7111, https://doi.org/10.1093/nar/gkae417
The activity of CobB1 protein deacetylase contributes to nucleoid compaction in Streptomyces venezuelae spores by increasing HupS affinity for DNA
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7112–7128, https://doi.org/10.1093/nar/gkae418
Bioinformatic analysis of type III CRISPR systems reveals key properties and new effector families
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7129–7141, https://doi.org/10.1093/nar/gkae462
Nucleic Acid Enzymes
Structural and functional investigation of the DHH/DHHA1 family proteins in Deinococcus radiodurans
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7142–7157, https://doi.org/10.1093/nar/gkae451
Adaptation of a eukaryote-like ProRS to a prokaryote-like tRNAPro
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7158–7170, https://doi.org/10.1093/nar/gkae483
RNA and RNA-protein complexes
Massively parallel identification of sequence motifs triggering ribosome-associated mRNA quality control
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7171–7187, https://doi.org/10.1093/nar/gkae285
The RBPome of influenza A virus NP-mRNA reveals a role for TDP-43 in viral replication
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7188–7210, https://doi.org/10.1093/nar/gkae291
Epigenetic control of adaptive or homeostatic splicing during interval-training activities
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7211–7224, https://doi.org/10.1093/nar/gkae311
PRMT5-mediated arginine methylation of FXR1 is essential for RNA binding in cancer cells
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7225–7244, https://doi.org/10.1093/nar/gkae319
A nematode-specific ribonucleoprotein complex mediates interactions between the major nematode spliced leader snRNP and its target pre-mRNAs
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7245–7260, https://doi.org/10.1093/nar/gkae321
Increased PTCHD4 expression via m6A modification of PTCHD4 mRNA promotes senescent cell survival
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7261–7278, https://doi.org/10.1093/nar/gkae322
Molecular mechanism for target RNA recognition and cleavage of Cas13h
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7279–7291, https://doi.org/10.1093/nar/gkae324
Structural Biology
Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7292–7304, https://doi.org/10.1093/nar/gkae374
Structural characterization of two prototypical repressors of SorC family reveals tetrameric assemblies on DNA and mechanism of function
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7305–7320, https://doi.org/10.1093/nar/gkae434
Insights into the molecular mechanism of ParABS system in chromosome partition by HpParA and HpParB
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7321–7336, https://doi.org/10.1093/nar/gkae450
DMC1 and RAD51 bind FxxA and FxPP motifs of BRCA2 via two separate interfaces
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7337–7353, https://doi.org/10.1093/nar/gkae452
Structure of the E. coli nucleoid-associated protein YejK reveals a novel DNA binding clamp
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7354–7366, https://doi.org/10.1093/nar/gkae459
Synthetic Biology and Bioengineering
LowTempGAL: a highly responsive low temperature-inducible GAL system in Saccharomyces cerevisiae
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7367–7383, https://doi.org/10.1093/nar/gkae460
Modular CRISPR/Cas12a synergistic activation platform for detection and logic operations
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Pages 7384–7396, https://doi.org/10.1093/nar/gkae470
Corrections
Correction to ‘The BRCA2 R2645G variant increases DNA binding and induces hyper-recombination’
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Page 7397, https://doi.org/10.1093/nar/gkae482
Correction to ‘MCPIP1 ribonuclease exhibits broad-spectrum antiviral effects through viral RNA binding and degradation’
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Page 7398, https://doi.org/10.1093/nar/gkae488
Methods
Liam tackles complex multimodal single-cell data integration challenges
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Page e52, https://doi.org/10.1093/nar/gkae409
mosaicMPI: a framework for modular data integration across cohorts and -omics modalities
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Page e53, https://doi.org/10.1093/nar/gkae442
Biochemical properties of chromatin domains define genome compartmentalization
Nucleic Acids Research, Volume 52, Issue 12, 8 July 2024, Page e54, https://doi.org/10.1093/nar/gkae454
