Volume 52, Issue 13
22 July 2024
Cover image
Cover image
Cover: The transcriptional corepressor IRF2BP2 interacts with the AP-1 transcription factor ATF7/JDP2 to suppress inflammatory pathways in AML cells. The cover shows an artistic representation of the ATF7/JDP2-IRF2BP2 complex on DNA, based on an AlphaFold 3 model.
For more information see article by Fischer, S. et al., pages 7590–7609 in this issue.
For more information see article by Fischer, S. et al., pages 7590–7609 in this issue.
ISSN 0305-1048
EISSN 1362-4962
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Volume 52, Issue 13, 22 July 2024
Editorial
Editorial: Gary Felsenfeld (1929–2024)
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7399–7400, https://doi.org/10.1093/nar/gkae503
Chemical Biology and Nucleic Acid Chemistry
YY1 is involved in homologous recombination inhibition at guanine quadruplex sites in human cells
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7401–7413, https://doi.org/10.1093/nar/gkae502
Formation of left-handed helices by C2′-fluorinated nucleic acids under physiological salt conditions
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7414–7428, https://doi.org/10.1093/nar/gkae508
Nanopores map the acid-base properties of a single site in a single DNA molecule
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7429–7436, https://doi.org/10.1093/nar/gkae518
Promoter dependent RNA polymerase II bypass of the epimerizable DNA lesion, Fapy•dG and 8-Oxo-2′-deoxyguanosine
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7437–7446, https://doi.org/10.1093/nar/gkae529
Computational Biology
Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7447–7464, https://doi.org/10.1093/nar/gkae500
Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA–ligand interactions
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7465–7486, https://doi.org/10.1093/nar/gkae541
Data Resources and Analyses
A treasure trove of 1034 actinomycete genomes
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7487–7503, https://doi.org/10.1093/nar/gkae523
Refining the pool of RNA-binding domains advances the classification and prediction of RNA-binding proteins
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7504–7522, https://doi.org/10.1093/nar/gkae536
A comprehensive analysis of 3′UTRs in Caenorhabditis elegans
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7523–7538, https://doi.org/10.1093/nar/gkae543
Gene Regulation, Chromatin and Epigenetics
Transposon DNA sequences facilitate the tissue-specific gene transfer of circulating tumor DNA between human cells
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7539–7555, https://doi.org/10.1093/nar/gkae427
Histone deacetylase Hos2 regulates protein expression noise by potentially modulating the protein translation machinery
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7556–7571, https://doi.org/10.1093/nar/gkae432
Repression of pervasive antisense transcription is the primary role of fission yeast RNA polymerase II CTD serine 2 phosphorylation
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7572–7589, https://doi.org/10.1093/nar/gkae436
IRF2BP2 counteracts the ATF7/JDP2 AP-1 heterodimer to prevent inflammatory overactivation in acute myeloid leukemia (AML) cells
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7590–7609, https://doi.org/10.1093/nar/gkae437
The developmental and evolutionary characteristics of transcription factor binding site clustered regions based on an explainable machine learning model
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7610–7626, https://doi.org/10.1093/nar/gkae441
RETRACTED AND REPLACED: Genomic context-dependent histone H3K36 methylation by three Drosophila methyltransferases and implications for dedicated chromatin readers
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7627–7649, https://doi.org/10.1093/nar/gkae449
Genome Integrity, Repair and Replication
Replication protein A dynamically re-organizes on primer/template junctions to permit DNA polymerase δ holoenzyme assembly and initiation of DNA synthesis
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7650–7664, https://doi.org/10.1093/nar/gkae475
KDM6A–SND1 interaction maintains genomic stability by protecting the nascent DNA and contributes to cancer chemoresistance
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7665–7686, https://doi.org/10.1093/nar/gkae487
RAD18 directs DNA double-strand break repair by homologous recombination to post-replicative chromatin
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7687–7703, https://doi.org/10.1093/nar/gkae499
Binding of the TRF2 iDDR motif to RAD50 highlights a convergent evolutionary strategy to inactivate MRN at telomeres
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7704–7719, https://doi.org/10.1093/nar/gkae509
Genomics
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7720–7739, https://doi.org/10.1093/nar/gkae540
ONECUT2 acts as a lineage plasticity driver in adenocarcinoma as well as neuroendocrine variants of prostate cancer
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7740–7760, https://doi.org/10.1093/nar/gkae547
Molecular Biology
Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7761–7779, https://doi.org/10.1093/nar/gkae448
Phage-host co-evolution has led to distinct generalized transduction strategies
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7780–7791, https://doi.org/10.1093/nar/gkae489
The impact of mRNA poly(A) tail length on eukaryotic translation stages
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7792–7808, https://doi.org/10.1093/nar/gkae510
Intrinsically disordered regions regulate RhlE RNA helicase functions in bacteria
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7809–7824, https://doi.org/10.1093/nar/gkae511
Nucleic Acid Enzymes
Eukaryotic AlaX provides multiple checkpoints for quality and quantity of aminoacyl-tRNAs in translation
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7825–7842, https://doi.org/10.1093/nar/gkae486
A Plasmodium apicoplast-targeted unique exonuclease/FEN exhibits interspecies functional differences attributable to an insertion that alters DNA-binding
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7843–7862, https://doi.org/10.1093/nar/gkae512
Coordinated DNA polymerization by Polγ and the region of LonP1 regulated proteolysis
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7863–7875, https://doi.org/10.1093/nar/gkae539
RNA and RNA-protein complexes
A novel regulatory interplay between atypical B12 riboswitches and uORF translation in Mycobacterium tuberculosis
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7876–7892, https://doi.org/10.1093/nar/gkae338
The uS10c-BPG2 module mediates ribosomal RNA processing in chloroplast nucleoids
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7893–7909, https://doi.org/10.1093/nar/gkae339
Genome-wide analysis of mRNA decay in Arabidopsis shoot and root reveals the importance of co-translational mRNA decay in the general mRNA turnover
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7910–7924, https://doi.org/10.1093/nar/gkae363
Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7925–7946, https://doi.org/10.1093/nar/gkae365
Structural Biology
YjgA plays dual roles in enhancing PTC maturation
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7947–7960, https://doi.org/10.1093/nar/gkae469
Crystal structure of a tetrameric RNA G-quadruplex formed by hexanucleotide repeat expansions of C9orf72 in ALS/FTD
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7961–7970, https://doi.org/10.1093/nar/gkae473
The 5′-terminal stem–loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7971–7986, https://doi.org/10.1093/nar/gkae477
Cooperative Gsx2–DNA binding requires DNA bending and a novel Gsx2 homeodomain interface
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7987–8002, https://doi.org/10.1093/nar/gkae522
Synthetic Biology and Bioengineering
OptoLacI: optogenetically engineered lactose operon repressor LacI responsive to light instead of IPTG
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 8003–8016, https://doi.org/10.1093/nar/gkae479
Engineering spacer specificity of the Cre/loxP system
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 8017–8031, https://doi.org/10.1093/nar/gkae481
Corrections
Correction to ‘YASS: enhancing the sensitivity of DNA similarity search’
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Page 8032, https://doi.org/10.1093/nar/gkae513
Correction to ‘N2-methylguanosine modifications on human tRNAs and snRNA U6 are important for cell proliferation, protein translation and pre-mRNA splicing’
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Page 8033, https://doi.org/10.1093/nar/gkae524
Correction to ‘hnRNPA1 couples nuclear export and translation of specific mRNAs downstream of FGF-2/S6K2 signalling’
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Page 8034, https://doi.org/10.1093/nar/gkae525
Correction to ‘Overexpression of eIF5 or its protein mimic 5MP perturbs eIF2 function and induces ATF4 translation through delayed re-initiation’
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Page 8035, https://doi.org/10.1093/nar/gkae542
Correction to ‘Structure of an internal loop motif with three consecutive U·U mismatches from stem–loop 1 in the 3′-UTR of the SARS-CoV-2 genomic RNA’
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Page 8036, https://doi.org/10.1093/nar/gkae545
Correction to ‘Cooperative Gsx2–DNA binding requires DNA bending and a novel Gsx2 homeodomain interface’
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Page 8037, https://doi.org/10.1093/nar/gkae578
Correction to ‘KDM6A–SND1 interaction maintains genomic stability by protecting the nascent DNA and contributes to cancer chemoresistance’
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Page 8038, https://doi.org/10.1093/nar/gkae581
Methods
Induro-RT mediated circRNA-sequencing (IMCR-seq) enables comprehensive profiling of full-length and long circular RNAs from low input total RNA
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Page e55, https://doi.org/10.1093/nar/gkae465
iSuRe-HadCre is an essential tool for effective conditional genetics
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Page e56, https://doi.org/10.1093/nar/gkae472
CAbiNet: joint clustering and visualization of cells and genes for single-cell transcriptomics
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Page e57, https://doi.org/10.1093/nar/gkae480
Transfer learning for cross-context prediction of protein expression from 5’UTR sequence
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Page e58, https://doi.org/10.1093/nar/gkae491
FRET-guided modeling of nucleic acids
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Page e59, https://doi.org/10.1093/nar/gkae496
Reinventing gene expression connectivity through regulatory and spatial structural empowerment via principal node aggregation graph neural network
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Page e60, https://doi.org/10.1093/nar/gkae514
