Volume 50, Issue 13
22 July 2022
Cover image
Cover image
Cover: Work by Fleming et al. (pages 7570–7590) identifies the tRNA modifying enzyme MiaA as a tunable regulatory nexus linking protein translation, stress responses, and metabolism. The image illustrates the aberrant architecture of a biofilm (~5 cm wide) formed by Extraintestinal Pathogenic Escherichia coli in the absence of MiaA.
For more information see article by Fleming, B.A. et al., pages 7570–7590 in this issue.
For more information see article by Fleming, B.A. et al., pages 7570–7590 in this issue.
ISSN 0305-1048
EISSN 1362-4962
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Volume 50, Issue 13, 22 July 2022
Editorial
Editorial: Critical reviews and perspectives in Nucleic Acids Research
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Page 7201, https://doi.org/10.1093/nar/gkac598
NAR Breakthrough Article
Membrane-dependent relief of translation elongation arrest on pseudouridine- and N1-methyl-pseudouridine-modified mRNAs
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7202–7215, https://doi.org/10.1093/nar/gkab1241
Critical Reviews and Perspectives
Establishing an environment in which rigorous scientific inquiry is practiced: a personal journey
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7216–7223, https://doi.org/10.1093/nar/gkac526
Chemical Biology and Nucleic Acid Chemistry
Identification of nucleobase chemical modifications that reduce the hepatotoxicity of gapmer antisense oligonucleotides
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7224–7234, https://doi.org/10.1093/nar/gkac562
Conjugation of chemical handles and functional moieties to DNA during solid phase synthesis with sulfonyl azides
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7235–7246, https://doi.org/10.1093/nar/gkac566
Short LNA-modified oligonucleotide probes as efficient disruptors of DNA G-quadruplexes
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7247–7259, https://doi.org/10.1093/nar/gkac569
Computational Biology
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7260–7286, https://doi.org/10.1093/nar/gkac537
Quantitative contribution of the spacer length in the supercoiling-sensitivity of bacterial promoters
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7287–7297, https://doi.org/10.1093/nar/gkac579
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7298–7309, https://doi.org/10.1093/nar/gkac593
Data Resources and Analyses
Regulation of both transcription and RNA turnover contribute to germline specification
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7310–7325, https://doi.org/10.1093/nar/gkac542
Gene Regulation, Chromatin and Epigenetics
SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7326–7349, https://doi.org/10.1093/nar/gkac531
Dual role of histone variant H3.3B in spermatogenesis: positive regulation of piRNA transcription and implication in X-chromosome inactivation
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7350–7366, https://doi.org/10.1093/nar/gkac541
OCT4 activates a Suv39h1-repressive antisense lncRNA to couple histone H3 Lysine 9 methylation to pluripotency
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7367–7379, https://doi.org/10.1093/nar/gkac550
Characterization of an autonomous pathway complex that promotes flowering in Arabidopsis
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7380–7395, https://doi.org/10.1093/nar/gkac551
On the stability of stalled RNA polymerase and its removal by RapA
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7396–7405, https://doi.org/10.1093/nar/gkac558
Genome Integrity, Repair and Replication
A combinatorial system to examine the enzymatic repair of multiply damaged DNA substrates
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7406–7419, https://doi.org/10.1093/nar/gkac530
Division of labor within the DNA damage tolerance system reveals non-epistatic and clinically actionable targets for precision cancer medicine
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7420–7435, https://doi.org/10.1093/nar/gkac545
Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7436–7450, https://doi.org/10.1093/nar/gkac555
Acetaldehyde makes a distinct mutation signature in single-stranded DNA
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7451–7464, https://doi.org/10.1093/nar/gkac570
Characterization of sequence contexts that favor alternative end joining at Cas9-induced double-strand breaks
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7465–7478, https://doi.org/10.1093/nar/gkac575
Genomics
De novo assembly of human genome at single-cell levels
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7479–7492, https://doi.org/10.1093/nar/gkac586
Molecular Biology
Selective pericentromeric heterochromatin dismantling caused by TP53 activation during senescence
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7493–7510, https://doi.org/10.1093/nar/gkac603
Nucleic Acid Enzymes
Quantitative parameters of bacterial RNA polymerase open-complex formation, stabilization and disruption on a consensus promoter
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7511–7528, https://doi.org/10.1093/nar/gkac560
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7529–7544, https://doi.org/10.1093/nar/gkac565
Phosphorylation of SAMHD1 Thr592 increases C-terminal domain dynamics, tetramer dissociation and ssDNA binding kinetics
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7545–7559, https://doi.org/10.1093/nar/gkac573
Direct adenylation from 5′-OH-terminated oligonucleotides by a fusion enzyme containing Pfu RNA ligase and T4 polynucleotide kinase
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7560–7569, https://doi.org/10.1093/nar/gkac604
RNA and RNA-protein complexes
A tRNA modifying enzyme as a tunable regulatory nexus for bacterial stress responses and virulence
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7570–7590, https://doi.org/10.1093/nar/gkac116
A novel, essential trans-splicing protein connects the nematode SL1 snRNP to the CBC-ARS2 complex
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7591–7607, https://doi.org/10.1093/nar/gkac534
LncRNA EPR-induced METTL7A1 modulates target gene translation
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7608–7622, https://doi.org/10.1093/nar/gkac544
P-bodies directly regulate MARF1-mediated mRNA decay in human cells
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7623–7636, https://doi.org/10.1093/nar/gkac557
Regulated dicing of pre-mir-144 via reshaping of its terminal loop
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7637–7654, https://doi.org/10.1093/nar/gkac568
Structural Biology
Molecular insights into the interaction of CAG trinucleotide RNA repeats with nucleolin and its implication in polyglutamine diseases
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7655–7668, https://doi.org/10.1093/nar/gkac532
Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7669–7679, https://doi.org/10.1093/nar/gkac548
Structural and functional characterization of DdrC, a novel DNA damage-induced nucleoid associated protein involved in DNA compaction
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7680–7696, https://doi.org/10.1093/nar/gkac563
Structural analysis of the basal state of the Artemis:DNA-PKcs complex
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7697–7720, https://doi.org/10.1093/nar/gkac564
Cryo neutron crystallography demonstrates influence of RNA 2′-OH orientation on conformation, sugar pucker and water structure
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7721–7738, https://doi.org/10.1093/nar/gkac577
Synthetic Biology and Bioengineering
Repurposing CRISPR RNA-guided integrases system for one-step, efficient genomic integration of ultra-long DNA sequences
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7739–7750, https://doi.org/10.1093/nar/gkac554
Activating natural product synthesis using CRISPR interference and activation systems in Streptomyces
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7751–7760, https://doi.org/10.1093/nar/gkac556
Large-scale genome editing based on high-capacity adenovectors and CRISPR-Cas9 nucleases rescues full-length dystrophin synthesis in DMD muscle cells
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7761–7782, https://doi.org/10.1093/nar/gkac567
Highly efficient CRISPR-mediated large DNA docking and multiplexed prime editing using a single baculovirus
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Pages 7783–7799, https://doi.org/10.1093/nar/gkac587
Retraction
Retraction of ‘Protein kinase CK2 phosphorylation regulates the interaction of Kaposi's sarcoma-associated herpesvirus regulatory protein ORF57 with its multifunctional partner hnRNP K’
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Page 7800, https://doi.org/10.1093/nar/gkac574
Methods Online
QRNAstruct: a method for extracting secondary structural features of RNA via regression with biological activity
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Page e73, https://doi.org/10.1093/nar/gkac220
A molecular beacon assay for monitoring RNA splicing
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Page e74, https://doi.org/10.1093/nar/gkac242
DEPhT: a novel approach for efficient prophage discovery and precise extraction
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Page e75, https://doi.org/10.1093/nar/gkac273
How clear is our current view on microbial dark matter? (Re-)assessing public MAG & SAG datasets with MDMcleaner
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Page e76, https://doi.org/10.1093/nar/gkac294
Efficient golden gate assembly of DNA constructs for single molecule force spectroscopy and imaging
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Page e77, https://doi.org/10.1093/nar/gkac300
Characterizing locus specific chromatin structure and dynamics with correlative conventional and super-resolution imaging in living cells
Nucleic Acids Research, Volume 50, Issue 13, 22 July 2022, Page e78, https://doi.org/10.1093/nar/gkac314
