Volume 50, Issue 15
26 August 2022
Cover image
Cover image
Cover: Alternative pre-mRNA splicing is key to proteome diversity. In this issue, Choi et al. identify that the TEAD1 splicing isoform regulated by RBFOX2 differentially affects the Hippo signaling pathway. The cover image illustrates the importance of splicing isoforms to enable fine-tuning of complex transcriptional programs by stably and precisely regulating signal transduction.
For more information see article by Choi, S. et al., pages 8658–8673 in this issue.
For more information see article by Choi, S. et al., pages 8658–8673 in this issue.
ISSN 0305-1048
EISSN 1362-4962
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Volume 50, Issue 15, 26 August 2022
NAR Breakthrough Article
A phage parasite deploys a nicking nuclease effector to inhibit viral host replication
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8401–8417, https://doi.org/10.1093/nar/gkac002
Chemical Biology and Nucleic Acid Chemistry
Intratracheally administered LNA gapmer antisense oligonucleotides induce robust gene silencing in mouse lung fibroblasts
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8418–8430, https://doi.org/10.1093/nar/gkac630
DNA circuits compatible encoder and demultiplexer based on a single biomolecular platform with DNA strands as outputs
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8431–8440, https://doi.org/10.1093/nar/gkac650
Computational Biology
Single base-pair resolution analysis of DNA binding motif with MoMotif reveals an oncogenic function of CTCF zinc-finger 1 mutation
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8441–8458, https://doi.org/10.1093/nar/gkac658
Molecular dynamics of DNA translocation by FtsK
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8459–8470, https://doi.org/10.1093/nar/gkac668
Gene Regulation, Chromatin and Epigenetics
The HDAC7–TET2 epigenetic axis is essential during early B lymphocyte development
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8471–8490, https://doi.org/10.1093/nar/gkac619
TET1 regulates gene expression and repression of endogenous retroviruses independent of DNA demethylation
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8491–8511, https://doi.org/10.1093/nar/gkac642
Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8512–8528, https://doi.org/10.1093/nar/gkac643
sRNA-controlled iron sparing response in Staphylococci
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8529–8546, https://doi.org/10.1093/nar/gkac648
SOX9 reprograms endothelial cells by altering the chromatin landscape
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8547–8565, https://doi.org/10.1093/nar/gkac652
The expression of aminoglycoside resistance genes in integron cassettes is not controlled by riboswitches
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8566–8579, https://doi.org/10.1093/nar/gkac662
The convergent xenogeneic silencer MucR predisposes α-proteobacteria to integrate AT-rich symbiosis genes
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8580–8598, https://doi.org/10.1093/nar/gkac664
SRRM2 organizes splicing condensates to regulate alternative splicing
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8599–8614, https://doi.org/10.1093/nar/gkac669
Widespread repression of anti-CRISPR production by anti-CRISPR-associated proteins
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8615–8625, https://doi.org/10.1093/nar/gkac674
Genome Integrity, Repair and Replication
Resistance of mitochondrial DNA to cadmium and Aflatoxin B1 damage-induced germline mutation accumulation in C. elegans
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8626–8642, https://doi.org/10.1093/nar/gkac666
Role for DNA double strand end-resection activity of RecBCD in control of aberrant chromosomal replication initiation in Escherichia coli
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8643–8657, https://doi.org/10.1093/nar/gkac670
Molecular Biology
RBFOX2-regulated TEAD1 alternative splicing plays a pivotal role in Hippo-YAP signaling
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8658–8673, https://doi.org/10.1093/nar/gkac509
CGG repeats trigger translational frameshifts that generate aggregation-prone chimeric proteins
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8674–8689, https://doi.org/10.1093/nar/gkac626
The L1-ORF1p coiled coil enables formation of a tightly compacted nucleic acid-bound complex that is associated with retrotransposition
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8690–8699, https://doi.org/10.1093/nar/gkac628
FACT subunit SUPT16H associates with BRD4 and contributes to silencing of interferon signaling
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8700–8718, https://doi.org/10.1093/nar/gkac645
Structural basis of DNA packaging by a ring-type ATPase from an archetypal viral system
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8719–8732, https://doi.org/10.1093/nar/gkac647
Nucleic Acid Enzymes
Top3α is the replicative topoisomerase in mitochondrial DNA replication
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8733–8748, https://doi.org/10.1093/nar/gkac660
Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for mtDNA replication completion
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8749–8766, https://doi.org/10.1093/nar/gkac661
Strand switching mechanism of Pif1 helicase induced by its collision with a G-quadruplex embedded in dsDNA
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8767–8778, https://doi.org/10.1093/nar/gkac667
RNA and RNA-protein complexes
MPP6 stimulates both RRP6 and DIS3 to degrade a specified subset of MTR4-sensitive substrates in the human nucleus
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8779–8806, https://doi.org/10.1093/nar/gkac559
Identification of a novel deFADding activity in human, yeast and bacterial 5′ to 3′ exoribonucleases
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8807–8817, https://doi.org/10.1093/nar/gkac617
Precise tuning of bacterial translation initiation by non-equilibrium 5′-UTR unfolding observed in single mRNAs
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8818–8833, https://doi.org/10.1093/nar/gkac635
Modeling splicing outcome by combining 5′ss strength and splicing regulatory elements
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8834–8851, https://doi.org/10.1093/nar/gkac663
SMG-6 mRNA cleavage stalls ribosomes near premature stop codons in vivo
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8852–8866, https://doi.org/10.1093/nar/gkac681
Structural Biology
Staggered intercalation of DNA duplexes with base-pair modulation by two distinct drug molecules induces asymmetric backbone twisting and structure polymorphism
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8867–8881, https://doi.org/10.1093/nar/gkac629
Structural assembly of the nucleic-acid-binding Thp3–Csn12–Sem1 complex functioning in mRNA splicing
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8882–8897, https://doi.org/10.1093/nar/gkac634
B-to-A transition in target DNA during retroviral integration
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8898–8918, https://doi.org/10.1093/nar/gkac644
Molecular basis of anti-CRISPR operon repression by Aca10
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8919–8928, https://doi.org/10.1093/nar/gkac656
FOXL2 and FOXA1 cooperatively assemble on the TP53 promoter in alternative dimer configurations
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8929–8946, https://doi.org/10.1093/nar/gkac673
Synthetic Biology and Bioengineering
Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8947–8960, https://doi.org/10.1093/nar/gkac649
A versatile Cas12k-based genetic engineering toolkit (C12KGET) for metabolic engineering in genetic manipulation-deprived strains
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8961–8973, https://doi.org/10.1093/nar/gkac655
Nonlinear manipulation and analysis of large DNA datasets
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8974–8985, https://doi.org/10.1093/nar/gkac672
CRISPR-RNAa: targeted activation of translation using dCas13 fusions to translation initiation factors
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Pages 8986–8998, https://doi.org/10.1093/nar/gkac680
Correction
Correction to ‘The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update’
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Page 8999, https://doi.org/10.1093/nar/gkac610
Correction to ‘TopDom: an efficient and deterministic method for identifying topological domains in genomes’
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Page 9000, https://doi.org/10.1093/nar/gkac654
Methods Online
ShapeSorter: a fully probabilistic method for detecting conserved RNA structure features supported by SHAPE evidence
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Page e85, https://doi.org/10.1093/nar/gkac405
Inference of cell state transitions and cell fate plasticity from single-cell with MARGARET
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Page e86, https://doi.org/10.1093/nar/gkac412
Organization of gene programs revealed by unsupervised analysis of diverse gene–trait associations
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Page e87, https://doi.org/10.1093/nar/gkac413
Detecting TAD-like domains from RNA-associated interactions
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Page e88, https://doi.org/10.1093/nar/gkac422
A novel, rapid and sensitive flow cytometry method reveals degradation of promoter proximal paused RNAPII in the presence and absence of UV
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Page e89, https://doi.org/10.1093/nar/gkac434
Functional editing of endogenous genes through rapid selection of cell pools (Rapid generation of endogenously tagged genes in Drosophila ovarian somatic sheath cells)
Nucleic Acids Research, Volume 50, Issue 15, 26 August 2022, Page e90, https://doi.org/10.1093/nar/gkac448
