Volume 50, Issue 17
23 September 2022
Cover image
Cover image
Cover: The combined actions of Argonaute10 (AGO10), the Hsp70/Hsp90 chaperone machinery, and inorganic phosphate allow plants to specifically recognize and regulate microRNA 165/166, a process essential to the maintenance of the shoot apical meristem.
For more information see article by Xiao, Y. et al., pages 10041–10052 in this issue.
For more information see article by Xiao, Y. et al., pages 10041–10052 in this issue.
ISSN 0305-1048
EISSN 1362-4962
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Volume 50, Issue 17, 23 September 2022
NAR Breakthrough Article
The consequences of differential origin licensing dynamics in distinct chromatin environments
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9601–9620, https://doi.org/10.1093/nar/gkac003
Chemical Biology and Nucleic Acid Chemistry
NMR determination of the 2:1 binding complex of naphthyridine carbamate dimer (NCD) and CGG/CGG triad in double-stranded DNA
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9621–9631, https://doi.org/10.1093/nar/gkac740
Small-molecule activators specific to adenine base editors through blocking the canonical TGF-β pathway
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9632–9646, https://doi.org/10.1093/nar/gkac742
Hybridization kinetics of out-of-equilibrium mixtures of short RNA oligonucleotides
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9647–9662, https://doi.org/10.1093/nar/gkac784
Crystallographic analysis of engineered polymerases synthesizing phosphonomethylthreosyl nucleic acid
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9663–9674, https://doi.org/10.1093/nar/gkac792
Computational Biology
Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9675–9688, https://doi.org/10.1093/nar/gkac743
Data Resources and Analyses
Global 5′-UTR RNA structure regulates translation of a SERPINA1 mRNA
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9689–9704, https://doi.org/10.1093/nar/gkac739
Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9705–9723, https://doi.org/10.1093/nar/gkac759
A spatiotemporal atlas of organogenesis in the development of orchid flowers
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9724–9737, https://doi.org/10.1093/nar/gkac773
Gene Regulation, Chromatin and Epigenetics
Chromatin fiber breaks into clutches under tension and crowding
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9738–9747, https://doi.org/10.1093/nar/gkac725
Dichotomous cis-regulatory motifs mediate the maturation of the neuromuscular junction by retrograde BMP signaling
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9748–9764, https://doi.org/10.1093/nar/gkac730
Mitochondrial stress induces AREG expression and epigenomic remodeling through c-JUN and YAP-mediated enhancer activation
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9765–9779, https://doi.org/10.1093/nar/gkac735
The androgen receptor couples promoter recruitment of RNA processing factors to regulation of alternative polyadenylation at the 3' end of transcripts
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9780–9796, https://doi.org/10.1093/nar/gkac737
The KdmB-EcoA-RpdA-SntB chromatin complex binds regulatory genes and coordinates fungal development with mycotoxin synthesis
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9797–9813, https://doi.org/10.1093/nar/gkac744
EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9814–9837, https://doi.org/10.1093/nar/gkac747
The high mobility group protein HMG20A cooperates with the histone reader PHF14 to modulate TGFβ and Hippo pathways
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9838–9857, https://doi.org/10.1093/nar/gkac766
Formation and removal of 1,N6-dimethyladenosine in mammalian transfer RNA
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9858–9872, https://doi.org/10.1093/nar/gkac770
Genome Integrity, Repair and Replication
Dynamic switching of crotonylation to ubiquitination of H2A at lysine 119 attenuates transcription–replication conflicts caused by replication stress
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9873–9892, https://doi.org/10.1093/nar/gkac734
Tracking of progressing human DNA polymerase δ holoenzymes reveals distributions of DNA lesion bypass activities
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9893–9908, https://doi.org/10.1093/nar/gkac745
Changes in the architecture and abundance of replication intermediates delineate the chronology of DNA damage tolerance pathways at UV-stalled replication forks in human cells
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9909–9929, https://doi.org/10.1093/nar/gkac746
Double-strand break toxicity is chromatin context independent
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9930–9947, https://doi.org/10.1093/nar/gkac758
Molecular Biology
Lamin A/C impairments cause mitochondrial dysfunction by attenuating PGC1α and the NAMPT-NAD+ pathway
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9948–9965, https://doi.org/10.1093/nar/gkac741
Plant mitochondrial RNA editing factors can perform targeted C-to-U editing of nuclear transcripts in human cells
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9966–9983, https://doi.org/10.1093/nar/gkac752
Widespread autogenous mRNA–protein interactions detected by CLIP-seq
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 9984–9999, https://doi.org/10.1093/nar/gkac756
Splicing of branchpoint-distant exons is promoted by Cactin, Tls1 and the ubiquitin-fold-activated Sde2
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 10000–10014, https://doi.org/10.1093/nar/gkac769
Nucleic Acid Enzymes
Human Thg1 displays tRNA-inducible GTPase activity
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 10015–10025, https://doi.org/10.1093/nar/gkac768
Mechanism of protein-primed template-independent DNA synthesis by Abi polymerases
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 10026–10040, https://doi.org/10.1093/nar/gkac772
RNA and RNA-protein complexes
The molecular mechanism of microRNA duplex selectivity of Arabidopsis ARGONAUTE10
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 10041–10052, https://doi.org/10.1093/nar/gkac571
Rbp95 binds to 25S rRNA helix H95 and cooperates with the Npa1 complex during early pre-60S particle maturation
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 10053–10077, https://doi.org/10.1093/nar/gkac724
Rotavirus RNA chaperone mediates global transcriptome-wide increase in RNA backbone flexibility
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 10078–10092, https://doi.org/10.1093/nar/gkac738
A 3′ UTR-derived small RNA connecting nitrogen and carbon metabolism in enteric bacteria
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 10093–10109, https://doi.org/10.1093/nar/gkac748
The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 10110–10122, https://doi.org/10.1093/nar/gkac751
Domain function and predicted structure of three heterodimeric endonuclease subunits of RNA editing catalytic complexes in Trypanosoma brucei
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 10123–10139, https://doi.org/10.1093/nar/gkac753
Three tRNA nuclear exporters in S. cerevisiae: parallel pathways, preferences, and precision
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 10140–10152, https://doi.org/10.1093/nar/gkac754
Allosteric activation of CRISPR-Cas12a requires the concerted movement of the bridge helix and helix 1 of the RuvC II domain
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 10153–10168, https://doi.org/10.1093/nar/gkac767
Structural Biology
Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 10169–10186, https://doi.org/10.1093/nar/gkac727
Synthetic Biology and Bioengineering
Yeast transcriptional device libraries enable precise synthesis of value-added chemicals from methanol
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Pages 10187–10199, https://doi.org/10.1093/nar/gkac765
Correction
Correction to ‘Staphylococcal self-loading helicases couple the staircase mechanism with inter domain high flexibility’
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Page 10200, https://doi.org/10.1093/nar/gkac818
Methods Online
DeNovoCNN: a deep learning approach to de novo variant calling in next generation sequencing data
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Page e97, https://doi.org/10.1093/nar/gkac511
Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Page e98, https://doi.org/10.1093/nar/gkac516
Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Page e99, https://doi.org/10.1093/nar/gkac517
Expansion microscopy allows high resolution single cell analysis of epigenetic readers
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Page e100, https://doi.org/10.1093/nar/gkac521
StrainXpress: strain aware metagenome assembly from short reads
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Page e101, https://doi.org/10.1093/nar/gkac543
A multiplexed, three-dimensional pooling and next-generation sequencing strategy for creating barcoded mutant arrays: construction of a Schizosaccharomyces pombe transposon insertion library
Nucleic Acids Research, Volume 50, Issue 17, 23 September 2022, Page e102, https://doi.org/10.1093/nar/gkac546
