Volume 50, Issue 6
8 April 2022
Cover image
Cover image
Cover: Bacterial viruses contain a dazzling variety of chemically complex modifications on their DNA. These non-canonical nucleotides inhibit a range of endonuclease based cellular defenses. It is now known that several types of virally encoded thymidine hypermodifications are derived from amino acids installed on DNA and further modified by a succession of enzyme types. These pathways have some product intermediates in common, including phosphorylated thymine, suggesting that base modifying biosynthetic pathways are modular, a possibility supported by the permuted combinations of hypermodification gene clusters observed in viral metagenome sequences from throughout the biosphere.
For more information see article by Lee, Y.-J. et al., pages 3001–3017 in this issue.
For more information see article by Lee, Y.-J. et al., pages 3001–3017 in this issue.
ISSN 0305-1048
EISSN 1362-4962
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Volume 50, Issue 6, 8 April 2022
NAR Breakthrough Article
Pathways of thymidine hypermodification
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3001–3017, https://doi.org/10.1093/nar/gkab781
Critical Reviews and Perspectives
RNA polymerase pausing, stalling and bypass during transcription of damaged DNA: from molecular basis to functional consequences
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3018–3041, https://doi.org/10.1093/nar/gkac174
Chemical Biology and Nucleic Acid Chemistry
Selective and stable base pairing by alkynylated nucleosides featuring a spatially-separated recognition interface
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3042–3055, https://doi.org/10.1093/nar/gkac140
7,8-Dihydro-8-oxo-1,N6-ethenoadenine: an exclusively Hoogsteen-paired thymine mimic in DNA that induces A→T transversions in Escherichia coli
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3056–3069, https://doi.org/10.1093/nar/gkac148
G-quadruplex inducer/stabilizer pyridostatin targets SUB1 to promote cytotoxicity of a transplatinum complex
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3070–3082, https://doi.org/10.1093/nar/gkac151
Programmable manipulation of oligonucleotide–albumin interaction for elongated circulation time
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3083–3095, https://doi.org/10.1093/nar/gkac156
Computational Biology
CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3096–3114, https://doi.org/10.1093/nar/gkac114
Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3115–3127, https://doi.org/10.1093/nar/gkac141
Predicting exon criticality from protein sequence
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3128–3141, https://doi.org/10.1093/nar/gkac155
DNAcycP: a deep learning tool for DNA cyclizability prediction
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3142–3154, https://doi.org/10.1093/nar/gkac162
Data Resources and Analyses
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3155–3168, https://doi.org/10.1093/nar/gkac163
Gene Regulation, Chromatin and Epigenetics
The DNA dioxygenase Tet1 regulates H3K27 modification and embryonic stem cell biology independent of its catalytic activity
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3169–3189, https://doi.org/10.1093/nar/gkac089
Role of the cellular factor CTCF in the regulation of bovine leukemia virus latency and three-dimensional chromatin organization
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3190–3202, https://doi.org/10.1093/nar/gkac107
Comparison of genome architecture at two stages of male germline cell differentiation in Drosophila
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3203–3225, https://doi.org/10.1093/nar/gkac109
Genome-wide characterization of i-motifs and their potential roles in the stability and evolution of transposable elements in rice
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3226–3238, https://doi.org/10.1093/nar/gkac121
Determinants of heritable gene silencing for KRAB-dCas9 + DNMT3 and Ezh2-dCas9 + DNMT3 hit-and-run epigenome editing
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3239–3253, https://doi.org/10.1093/nar/gkac123
Molecular basis of crosstalk in nuclear receptors: heterodimerization between PXR and CAR and the implication in gene regulation
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3254–3275, https://doi.org/10.1093/nar/gkac133
Cdc48Ufd1/Npl4 segregase removes mislocalized centromeric histone H3 variant CENP-A from non-centromeric chromatin
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3276–3291, https://doi.org/10.1093/nar/gkac135
8-oxodG accumulation within super-enhancers marks fragile CTCF-mediated chromatin loops
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3292–3306, https://doi.org/10.1093/nar/gkac143
Chromatin landscape associated with sexual differentiation in a UV sex determination system
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3307–3322, https://doi.org/10.1093/nar/gkac145
BMAL1 moonlighting as a gatekeeper for LINE1 repression and cellular senescence in primates
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3323–3347, https://doi.org/10.1093/nar/gkac146
A mobile restriction–modification system provides phage defence and resolves an epigenetic conflict with an antagonistic endonuclease
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3348–3361, https://doi.org/10.1093/nar/gkac147
EWS splicing regulation contributes to balancing Foxp1 isoforms required for neuronal differentiation
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3362–3378, https://doi.org/10.1093/nar/gkac154
Dysregulated RNA polyadenylation contributes to metabolic impairment in non-alcoholic fatty liver disease
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3379–3393, https://doi.org/10.1093/nar/gkac165
The human AP-endonuclease 1 (APE1) is a DNA G-quadruplex structure binding protein and regulates KRAS expression in pancreatic ductal adenocarcinoma cells
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3394–3412, https://doi.org/10.1093/nar/gkac172
Genome-wide landscape of ApiAP2 transcription factors reveals a heterochromatin-associated regulatory network during Plasmodium falciparum blood-stage development
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3413–3431, https://doi.org/10.1093/nar/gkac176
Genome Integrity, Repair and Replication
The RecD2 helicase balances RecA activities
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3432–3444, https://doi.org/10.1093/nar/gkac131
i-Motif formation and spontaneous deletions in human cells
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3445–3455, https://doi.org/10.1093/nar/gkac158
Genomics
Global chromosome rearrangement induced by CRISPR-Cas9 reshapes the genome and transcriptome of human cells
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3456–3474, https://doi.org/10.1093/nar/gkac153
RNA and RNA-protein complexes
Nanopore ReCappable sequencing maps SARS-CoV-2 5′ capping sites and provides new insights into the structure of sgRNAs
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3475–3489, https://doi.org/10.1093/nar/gkac144
Retron reverse transcriptase termination and phage defense are dependent on host RNase H1
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3490–3504, https://doi.org/10.1093/nar/gkac177
Structural Biology
The MYC oncoprotein directly interacts with its chromatin cofactor PNUTS to recruit PP1 phosphatase
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3505–3522, https://doi.org/10.1093/nar/gkac138
Synthetic Biology and Bioengineering
Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3523–3534, https://doi.org/10.1093/nar/gkac142
High-throughput screening of cell-free riboswitches by fluorescence-activated droplet sorting
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3535–3550, https://doi.org/10.1093/nar/gkac152
Predicting base editing outcomes using position-specific sequence determinants
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3551–3564, https://doi.org/10.1093/nar/gkac161
A cytosine base editor toolkit with varying activity windows and target scopes for versatile gene manipulation in plants
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3565–3580, https://doi.org/10.1093/nar/gkac166
Activating cryptic biosynthetic gene cluster through a CRISPR–Cas12a-mediated direct cloning approach
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3581–3592, https://doi.org/10.1093/nar/gkac181
Correction
Correction to ‘Stabilization of SMAR1 mRNA by PGA2 involves a stem–loop structure in the 5′ UTR’
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3593–3596, https://doi.org/10.1093/nar/gkac168
Correction to ‘Impaired in vivo binding of MeCP2 to chromatin in the absence of its DNA methyl-binding domain’
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3597–3598, https://doi.org/10.1093/nar/gkac169
Correction to ‘MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain’
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Pages 3599–3600, https://doi.org/10.1093/nar/gkac204
Methods Online
A simple and general approach to generate photoactivatable DNA processing enzymes
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Page e31, https://doi.org/10.1093/nar/gkab1212
Mutation enrichment in human DNA samples via UV-mediated cross-linking
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Page e32, https://doi.org/10.1093/nar/gkab1222
Locus-specific chromatin profiling of evolutionarily young transposable elements
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Page e33, https://doi.org/10.1093/nar/gkab1232
Deviation from baseline mutation burden provides powerful and robust rare-variants association test for complex diseases
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Page e34, https://doi.org/10.1093/nar/gkab1234
HiCRes: a computational method to estimate and predict the genomic resolution of Hi-C libraries
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Page e35, https://doi.org/10.1093/nar/gkab1235
GIP: an open-source computational pipeline for mapping genomic instability from protists to cancer cells
Nucleic Acids Research, Volume 50, Issue 6, 8 April 2022, Page e36, https://doi.org/10.1093/nar/gkab1237
