Volume 50, Issue 3
22 February 2022
Cover image
Cover image
Cover: The crystal structure of human Argonaute2 (Ago2) bound to miR-20a is shown with the various domains and linkers in the ribbon diagram highlighted in different colors and the active site indicated. The four insets depict (counterclockwise from bottom left) the environments of (i) phosphate P2 (between N1 and N2 nucleotides) bound to the MID domain (matching olive frame), (ii) phosphate P23 (between N22 and N23 nucleotides) bound to the PAZ domain (matching red frame), (iii) phosphate at the active site of the 5′→3′ exonuclease RNase J, and (iv) phosphate at the active site of the 3′→5′ exonuclease domain of DNA Pol I Klenow fragment (matching yellow frames). The pro-Rp and pro-Sp oxygens at the binding/active sites are drawn as spheres colored in pink and cyan, respectively. The Rp PS is preferred atMID for Ago2 mediated silencing activity and offers better protection against 5′-exonuclease degradation. The Sp PS is preferred at PAZ for Ago2 while offering better protection against 3′-exonuclease degradation.
For more information see article by Jahns, H. et al., pages 1221–1240 in this issue.
For more information see article by Jahns, H. et al., pages 1221–1240 in this issue.
ISSN 0305-1048
EISSN 1362-4962
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Volume 50, Issue 3, 22 February 2022
NAR Breakthrough Article
Adenovirus prevents dsRNA formation by promoting efficient splicing of viral RNA
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1201–1220, https://doi.org/10.1093/nar/gkab896
Chemical Biology and Nucleic Acid Chemistry
Chirality matters: stereo-defined phosphorothioate linkages at the termini of small interfering RNAs improve pharmacology in vivo
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1221–1240, https://doi.org/10.1093/nar/gkab544
Supramolecular CRISPR-OFF switches with host–guest chemistry
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1241–1255, https://doi.org/10.1093/nar/gkac008
CRISPR–Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1256–1268, https://doi.org/10.1093/nar/gkac049
Computational Biology
DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1269–1279, https://doi.org/10.1093/nar/gkab1252
Variational autoencoding of gene landscapes during mouse CNS development uncovers layered roles of Polycomb Repressor Complex 2
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1280–1296, https://doi.org/10.1093/nar/gkac006
Modeling the ribosomal small subunit dynamic in Saccharomyces cerevisiae based on TCP-seq data
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1297–1316, https://doi.org/10.1093/nar/gkac021
Data Resources and Analyses
The fork protection complex recruits FACT to reorganize nucleosomes during replication
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1317–1334, https://doi.org/10.1093/nar/gkac005
Polympact: exploring functional relations among common human genetic variants
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1335–1350, https://doi.org/10.1093/nar/gkac024
Waves of sumoylation support transcription dynamics during adipocyte differentiation
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1351–1369, https://doi.org/10.1093/nar/gkac027
Gene Regulation, Chromatin and Epigenetics
Vimentin binds to G-quadruplex repeats found at telomeres and gene promoters
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1370–1381, https://doi.org/10.1093/nar/gkab1274
Thyroid hormone dependent transcriptional programming by TRβ requires SWI/SNF chromatin remodelers
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1382–1395, https://doi.org/10.1093/nar/gkab1287
Nuclear and cytoplasmic RNA exosomes and PELOTA1 prevent miRNA-induced secondary siRNA production in Arabidopsis
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1396–1415, https://doi.org/10.1093/nar/gkab1289
piRNAs of Caenorhabditis elegans broadly silence nonself sequences through functionally random targeting
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1416–1429, https://doi.org/10.1093/nar/gkab1290
Modulated termination of non-coding transcription partakes in the regulation of gene expression
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1430–1448, https://doi.org/10.1093/nar/gkab1304
A complex network of interactions governs DNA methylation at telomeric regions
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1449–1464, https://doi.org/10.1093/nar/gkac012
Genome Integrity, Repair and Replication
53BP1-ACLY-SLBP-coordinated activation of replication-dependent histone biogenesis maintains genomic integrity
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1465–1483, https://doi.org/10.1093/nar/gkab1300
Characterization of the SARS-CoV-2 ExoN (nsp14ExoN–nsp10) complex: implications for its role in viral genome stability and inhibitor identification
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1484–1500, https://doi.org/10.1093/nar/gkab1303
TOPORS-mediated RAD51 SUMOylation facilitates homologous recombination repair
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1501–1516, https://doi.org/10.1093/nar/gkac009
TRIM21 suppresses CHK1 activation by preferentially targeting CLASPIN for K63-linked ubiquitination
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1517–1530, https://doi.org/10.1093/nar/gkac011
Genomics
Diverse DNA modification in marine prokaryotic and viral communities
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1531–1550, https://doi.org/10.1093/nar/gkab1292
Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1551–1561, https://doi.org/10.1093/nar/gkab1297
Molecular Biology
Unique properties of spacer acquisition by the type III-A CRISPR-Cas system
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1562–1582, https://doi.org/10.1093/nar/gkab1193
Rapid factor depletion highlights intricacies of nucleoplasmic RNA degradation
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1583–1600, https://doi.org/10.1093/nar/gkac001
Structural characterization of a new subclass of panicum mosaic virus-like 3′ cap-independent translation enhancer
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1601–1619, https://doi.org/10.1093/nar/gkac007
Cytoplasmic switch of ARS2 isoforms promotes nonsense-mediated mRNA decay and arsenic sensitivity
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1620–1638, https://doi.org/10.1093/nar/gkac033
Nucleic Acid Enzymes
The C nucleotide at the mature 5′ end of the Escherichia coli proline tRNAs is required for the RNase E cleavage specificity at the 3′ terminus as well as functionality
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1639–1649, https://doi.org/10.1093/nar/gkab1260
High-fidelity KKH variant of Staphylococcus aureus Cas9 nucleases with improved base mismatch discrimination
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1650–1660, https://doi.org/10.1093/nar/gkab1291
Different modes of spacer acquisition by the Staphylococcus epidermidis type III-A CRISPR-Cas system
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1661–1672, https://doi.org/10.1093/nar/gkab1299
Experimental demonstration of operon formation catalyzed by insertion sequence
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1673–1686, https://doi.org/10.1093/nar/gkac004
RNA and RNA-protein complexes
Identification, functional characterization, assembly and structure of ToxIN type III toxin–antitoxin complex from E. coli
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1687–1700, https://doi.org/10.1093/nar/gkab1264
Selection and identification of an RNA aptamer that specifically binds the HIV-1 capsid lattice and inhibits viral replication
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1701–1717, https://doi.org/10.1093/nar/gkab1293
Multiple in vivo roles for the C-terminal domain of the RNA chaperone Hfq
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1718–1733, https://doi.org/10.1093/nar/gkac017
Dicer dependent tRNA derived small RNAs promote nascent RNA silencing
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1734–1752, https://doi.org/10.1093/nar/gkac022
Structural Biology
Mechanisms of Cre recombinase synaptic complex assembly and activation illuminated by Cryo-EM
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1753–1769, https://doi.org/10.1093/nar/gkac032
Cryo-EM structure of the ancient eukaryotic ribosome from the human parasite Giardia lamblia
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1770–1782, https://doi.org/10.1093/nar/gkac046
Synthetic Biology and Bioengineering
A modular RNA interference system for multiplexed gene regulation
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1783–1793, https://doi.org/10.1093/nar/gkab1301
Correction
Correction to ‘RiboVIEW: a computational framework for visualization, quality control and statistical analysis of ribosome profiling data’
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Page 1794, https://doi.org/10.1093/nar/gkac031
Correction to ‘TREND: a platform for exploring protein function in prokaryotes based on phylogenetic, domain architecture and gene neighborhood analyses’
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Page 1795, https://doi.org/10.1093/nar/gkac034
Correction to ‘The human insulin receptor mRNA contains a functional internal ribosome entry segment’
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1796–1798, https://doi.org/10.1093/nar/gkac063
Correction to ‘Bias-minimized quantification of microRNA reveals widespread alternative processing and 3′ end modification’
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Pages 1799–1800, https://doi.org/10.1093/nar/gkac078
Methods Online
Genome-wide mapping of G-quadruplex structures with CUT&Tag
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Page e13, https://doi.org/10.1093/nar/gkab1073
UFold: fast and accurate RNA secondary structure prediction with deep learning
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Page e14, https://doi.org/10.1093/nar/gkab1074
Improved dsDNA recombineering enables versatile multiplex genome engineering of kilobase-scale sequences in diverse bacteria
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Page e15, https://doi.org/10.1093/nar/gkab1076
From genotype to phenotype in Arabidopsis thaliana: in-silico genome interpretation predicts 288 phenotypes from sequencing data
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Page e16, https://doi.org/10.1093/nar/gkab1099
Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Page e17, https://doi.org/10.1093/nar/gkab1115
Isocratic HPLC analysis for the simultaneous determination of dNTPs, rNTPs and ADP in biological samples
Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Page e18, https://doi.org/10.1093/nar/gkab1117
