Volume 51, Issue 18
13 October 2023
Cover image
Cover image
Cover: Illustration of mixed DNA from different entities, representing the potential genetic innovation caused by the mixture of DNA from distinct genomic sources (chimeras). In this issue, Oliveira et al. developed a pipeline named ChimeraTE to detect chimeric transcripts, which are mixed mRNA with sequences derived from genes and transposable elements (TEs). In this cover image, the digital artist Kirunarin re-imagines the biological phenomenon of generating chimeras as the Greek chimera “Chimæra”.
For more information see article by Oliveira, D.S. et al., pages 9764–9784 in this issue.
For more information see article by Oliveira, D.S. et al., pages 9764–9784 in this issue.
ISSN 0305-1048
EISSN 1362-4962
Issue navigation
Volume 51, Issue 18, 13 October 2023
NAR Breakthrough Article
Assessing in vivo the impact of gene context on transcription through DNA supercoiling
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9509–9521, https://doi.org/10.1093/nar/gkad688
Critical Reviews and Perspectives
When will RNA get its AlphaFold moment?
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9522–9532, https://doi.org/10.1093/nar/gkad726
Chemical Biology and Nucleic Acid Chemistry
Photoswitchable molecular glue for RNA: reversible photocontrol of structure and function of the ribozyme
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9533–9541, https://doi.org/10.1093/nar/gkad690
Stability and mechanism of threose nucleic acid toward acid-mediated degradation
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9542–9551, https://doi.org/10.1093/nar/gkad716
Computational Biology
Assessing base-resolution DNA mechanics on the genome scale
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9552–9566, https://doi.org/10.1093/nar/gkad720
RIBFIND2: Identifying rigid bodies in protein and nucleic acid structures
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9567–9575, https://doi.org/10.1093/nar/gkad721
Gene Regulation, Chromatin and Epigenetics
PAXIP1 and STAG2 converge to maintain 3D genome architecture and facilitate promoter/enhancer contacts to enable stress hormone-dependent transcription
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9576–9593, https://doi.org/10.1093/nar/gkad267
CRISPR screens in sister chromatid cohesion defective cells reveal PAXIP1-PAGR1 as regulator of chromatin association of cohesin
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9594–9609, https://doi.org/10.1093/nar/gkad756
TDP-1 and FUST-1 co-inhibit exon inclusion and control fertility together with transcriptional regulation
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9610–9628, https://doi.org/10.1093/nar/gkad665
DNA mimic foldamers affect chromatin composition and disturb cell cycle progression
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9629–9642, https://doi.org/10.1093/nar/gkad681
Yeast transcription factor Msn2 binds to G4 DNA
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9643–9657, https://doi.org/10.1093/nar/gkad684
Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9658–9671, https://doi.org/10.1093/nar/gkad695
New twists of a TAIL: novel insights into the histone binding properties of a highly conserved PHD finger cluster within the MLR family of H3K4 mono-methyltransferases
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9672–9689, https://doi.org/10.1093/nar/gkad698
Optimisation of TP53 reporters by systematic dissection of synthetic TP53 response elements
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9690–9702, https://doi.org/10.1093/nar/gkad718
Genome Integrity, Repair and Replication
Recombinase-independent chromosomal rearrangements between dispersed inverted repeats in Saccharomyces cerevisiae meiosis
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9703–9715, https://doi.org/10.1093/nar/gkad650
Structure-specific roles for PolG2–DNA complexes in maintenance and replication of mitochondrial DNA
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9716–9732, https://doi.org/10.1093/nar/gkad679
RAP80 phase separation at DNA double-strand break promotes BRCA1 recruitment
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9733–9747, https://doi.org/10.1093/nar/gkad686
DONSON facilitates Cdc45 and GINS chromatin association and is essential for DNA replication initiation
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9748–9763, https://doi.org/10.1093/nar/gkad694
Genomics
ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9764–9784, https://doi.org/10.1093/nar/gkad671
The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9785–9803, https://doi.org/10.1093/nar/gkad685
Molecular Biology
Bacillus subtilis NrnB is expressed during sporulation and acts as a unique 3′-5′ exonuclease
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9804–9820, https://doi.org/10.1093/nar/gkad662
tRNA queuosine modification is involved in biofilm formation and virulence in bacteria
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9821–9837, https://doi.org/10.1093/nar/gkad667
Translocating RNA polymerase generates R-loops at DNA double-strand breaks without any additional factors
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9838–9848, https://doi.org/10.1093/nar/gkad689
Lipid kinase PIP5K1A regulates let-7 microRNA biogenesis through interacting with nuclear export protein XPO5
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9849–9862, https://doi.org/10.1093/nar/gkad709
ZEB1 promotes non-homologous end joining double-strand break repair
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9863–9879, https://doi.org/10.1093/nar/gkad723
Nucleic Acid Enzymes
Guide-specific loss of efficiency and off-target reduction with Cas9 variants
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9880–9893, https://doi.org/10.1093/nar/gkad702
Unidirectional trans-cleaving behavior of CRISPR-Cas12a unlocks for an ultrasensitive assay using hybrid DNA reporters containing a 3′ toehold
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9894–9904, https://doi.org/10.1093/nar/gkad715
Genome-wide screening reveals metabolic regulation of stop-codon readthrough by cyclic AMP
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9905–9919, https://doi.org/10.1093/nar/gkad725
Novobiocin blocks nucleic acid binding to Polθ and inhibits stimulation of its ATPase activity
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9920–9937, https://doi.org/10.1093/nar/gkad727
RNA and RNA-protein complexes
On the rules of engagement for microRNAs targeting protein coding regions
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9938–9951, https://doi.org/10.1093/nar/gkad645
Capturing heterogeneous conformers of cobalamin riboswitch by cryo-EM
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9952–9960, https://doi.org/10.1093/nar/gkad651
Cell-type specific regulator RBPMS switches alternative splicing via higher-order oligomerization and heterotypic interactions with other splicing regulators
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9961–9982, https://doi.org/10.1093/nar/gkad652
Increased levels of eIF2A inhibit translation by sequestering 40S ribosomal subunits
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9983–10000, https://doi.org/10.1093/nar/gkad683
Domain collapse and active site ablation generate a widespread animal mitochondrial seryl-tRNA synthetase
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 10001–10010, https://doi.org/10.1093/nar/gkad696
Structural Biology
Multivalency of nucleosome recognition by LEDGF
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 10011–10025, https://doi.org/10.1093/nar/gkad674
An archaeal transcription factor EnfR with a novel ‘eighth note’ fold controls hydrogen production of a hyperthermophilic archaeon Thermococcus onnurineus NA1
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 10026–10040, https://doi.org/10.1093/nar/gkad699
SARS-CoV-2 Nsp8 N-terminal domain folds autonomously and binds dsRNA
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 10041–10048, https://doi.org/10.1093/nar/gkad714
Structural basis of transcriptional activation by the OmpR/PhoB-family response regulator PmrA
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 10049–10058, https://doi.org/10.1093/nar/gkad724
Synthetic Biology and Bioengineering
Engineered lentivirus-derived nanoparticles (LVNPs) for delivery of CRISPR/Cas ribonucleoprotein complexes supporting base editing, prime editing and in vivo gene modification
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 10059–10074, https://doi.org/10.1093/nar/gkad676
Precise genome editing of the Kozak sequence enables bidirectional and quantitative modulation of protein translation to anticipated levels without affecting transcription
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 10075–10093, https://doi.org/10.1093/nar/gkad687
Strategies to identify and edit improvements in synthetic genome segments episomally
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 10094–10106, https://doi.org/10.1093/nar/gkad692
Correction
Correction to ‘In vivo analysis of Pim-1 deficiency’
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Page 10107, https://doi.org/10.1093/nar/gkad728
Expression of concern
Expression of concern on ‘Influence of correct secondary and tertiary RNA folding on the binding of cellular factors to the HCV IRES’
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Page 10108, https://doi.org/10.1093/nar/gkad749
Methods
Recovery of protein synthesis to assay DNA repair activity in transcribed genes in living cells and tissues
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Page e93, https://doi.org/10.1093/nar/gkad642
LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Page e94, https://doi.org/10.1093/nar/gkad664
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Page e95, https://doi.org/10.1093/nar/gkad693
SFyNCS detects oncogenic fusions involving non-coding sequences in cancer
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Page e96, https://doi.org/10.1093/nar/gkad705
Real-time imaging of drug-induced trapping of cellular topoisomerases and poly(ADP-ribose) polymerase 1 at the single-molecule level
Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Page e97, https://doi.org/10.1093/nar/gkad735
