Volume 47, Issue 6
08 April 2019
Cover image
Cover image
Cover: Chain-terminating nucleoside analogs (CTNAs) such as 2′,3′-dideoxycytidine, cytarabine and zidovudine, are widely used as antivirals or anticancer agents. When incorporated into DNA CTNAs cannot be extended by DNA polymerases, leading to arrested replication forks (DNA-combing), double-strand breaks (Neutral Comets), isochromatid fragility, and cell death. On page 2966–2980 Mohiuddin et al., reveal that the BRCA1–CtIP complex promotes MRE11 nuclease activity to remove incorporated CTNAs from nascent genomic DNA to permit tolerance to CTNAs. The cover image concept and art work is by Mohiuddin Mohiuddin and Christopher E. Pearson.
For more information see the article by Mohiuddin, M. et al., pages 2966–2980, in this issue.
For more information see the article by Mohiuddin, M. et al., pages 2966–2980, in this issue.
ISSN 0305-1048
EISSN 1362-4962
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Volume 47, Issue 6, 08 April 2019
NAR Breakthrough Article
The nuclear structural protein NuMA is a negative regulator of 53BP1 in DNA double-strand break repair
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2703–2715, https://doi.org/10.1093/nar/gkz138
Survey and Summary
Does co-transcriptional regulation of alternative splicing mediate plant stress responses?
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2716–2726, https://doi.org/10.1093/nar/gkz121
Chemical Biology and Nucleic Acid Chemistry
Cationic porphyrins with large side arm substituents as resonance light scattering ratiometric probes for specific recognition of nucleic acid G-quadruplexes
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2727–2738, https://doi.org/10.1093/nar/gkz064
Modulation of the ATM/autophagy pathway by a G-quadruplex ligand tips the balance between senescence and apoptosis in cancer cells
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2739–2756, https://doi.org/10.1093/nar/gkz095
Computational Biology
Targeted DNA oxidation and trajectory of radical DNA using DFT based QM/MM dynamics
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2757–2765, https://doi.org/10.1093/nar/gkz089
Chromatin organization modulates the origin of heritable structural variations in human genome
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2766–2777, https://doi.org/10.1093/nar/gkz103
Labelled regulatory elements are pervasive features of the macrophage genome and are dynamically utilized by classical and alternative polarization signals
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2778–2792, https://doi.org/10.1093/nar/gkz118
Gene Regulation, Chromatin and Epigenetics
Conformational changes and catalytic inefficiency associated with Mot1-mediated TBP–DNA dissociation
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2793–2806, https://doi.org/10.1093/nar/gky1322
Requirement for PRC1 subunit BMI1 in host gene activation by Epstein–Barr virus protein EBNA3C
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2807–2821, https://doi.org/10.1093/nar/gky1323
SMCHD1 is involved in de novo methylation of the DUX4-encoding D4Z4 macrosatellite
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2822–2839, https://doi.org/10.1093/nar/gkz005
RNF20/40-mediated eEF1BδL monoubiquitylation stimulates transcription of heat shock-responsive genes
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2840–2855, https://doi.org/10.1093/nar/gkz006
ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2856–2870, https://doi.org/10.1093/nar/gkz010
Evidence for a bind-then-bend mechanism for architectural DNA binding protein yNhp6A
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2871–2883, https://doi.org/10.1093/nar/gkz022
Human Survival Motor Neuron genes generate a vast repertoire of circular RNAs
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2884–2905, https://doi.org/10.1093/nar/gkz034
Genome Integrity, Repair and Replication
A genome-wide RNAi screen identifies the SMC5/6 complex as a non-redundant regulator of a Topo2a-dependent G2 arrest
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2906–2921, https://doi.org/10.1093/nar/gky1295
The lyase activity of bifunctional DNA glycosylases and the 3′-diesterase activity of APE1 contribute to the repair of oxidized bases in nucleosomes
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2922–2931, https://doi.org/10.1093/nar/gky1315
Broad range of missense error frequencies in cellular proteins
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2932–2945, https://doi.org/10.1093/nar/gky1319
RecFOR epistasis group: RecF and RecO have distinct localizations and functions in Escherichia coli
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2946–2965, https://doi.org/10.1093/nar/gkz003
CtIP-BRCA1 complex and MRE11 maintain replication forks in the presence of chain terminating nucleoside analogs
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2966–2980, https://doi.org/10.1093/nar/gkz009
Genomics
Significant abundance of cis configurations of coding variants in diploid human genomes
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2981–2995, https://doi.org/10.1093/nar/gkz031
Molecular Biology
Sas10 controls ribosome biogenesis by stabilizing Mpp10 and delivering the Mpp10–Imp3–Imp4 complex to nucleolus
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 2996–3012, https://doi.org/10.1093/nar/gkz105
Long noncoding RNA MALAT1 releases epigenetic silencing of HIV-1 replication by displacing the polycomb repressive complex 2 from binding to the LTR promoter
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3013–3027, https://doi.org/10.1093/nar/gkz117
Nucleic Acid Enzymes
Plant organellar DNA polymerases repair double-stranded breaks by microhomology-mediated end-joining
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3028–3044, https://doi.org/10.1093/nar/gkz039
RNA surveillance by uridylation-dependent RNA decay in Schizosaccharomyces pombe
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3045–3057, https://doi.org/10.1093/nar/gkz043
Single molecule glycosylase studies with engineered 8-oxoguanine DNA damage sites show functional defects of a MUTYH polyposis variant
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3058–3071, https://doi.org/10.1093/nar/gkz045
The G3-U70-independent tRNA recognition by human mitochondrial alanyl-tRNA synthetase
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3072–3085, https://doi.org/10.1093/nar/gkz078
RNA and RNA-protein complexes
Nuclear processing of nascent transcripts determines synthesis of full-length proteins and antigenic peptides
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3086–3100, https://doi.org/10.1093/nar/gky1296
Hidden sequence specificity in loading of single-stranded RNAs onto Drosophila Argonautes
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3101–3116, https://doi.org/10.1093/nar/gky1300
Molecular basis for transfer RNA recognition by the double-stranded RNA-binding domain of human dihydrouridine synthase 2
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3117–3126, https://doi.org/10.1093/nar/gky1302
YB-1, an abundant core mRNA-binding protein, has the capacity to form an RNA nucleoprotein filament: a structural analysis
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3127–3141, https://doi.org/10.1093/nar/gky1303
Structural insights reveal the specific recognition of roX RNA by the dsRNA-binding domains of the RNA helicase MLE and its indispensable role in dosage compensation in Drosophila
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3142–3157, https://doi.org/10.1093/nar/gky1308
Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3158–3170, https://doi.org/10.1093/nar/gky1311
Three autoinducer molecules act in concert to control virulence gene expression in Vibrio cholerae
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3171–3183, https://doi.org/10.1093/nar/gky1320
Reconstitution of the human SRP system and quantitative and systematic analysis of its ribosome interactions
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3184–3196, https://doi.org/10.1093/nar/gky1324
Structural Biology
A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3197–3207, https://doi.org/10.1093/nar/gkz002
Structural and functional analysis of the nucleotide and DNA binding activities of the human PIF1 helicase
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3208–3222, https://doi.org/10.1093/nar/gkz028
Understanding the role of intermolecular interactions between lissoclimides and the eukaryotic ribosome
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3223–3232, https://doi.org/10.1093/nar/gkz053
Alternative conformation induced by substrate binding for Arabidopsis thalianaN6-methyl-AMP deaminase
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3233–3243, https://doi.org/10.1093/nar/gkz070
Synthetic Biology and Bioengineering
A versatile platform strain for high-fidelity multiplex genome editing
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Pages 3244–3256, https://doi.org/10.1093/nar/gkz085
Methods Online
NextPBM: a platform to study cell-specific transcription factor binding and cooperativity
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Page e31, https://doi.org/10.1093/nar/gkz020
Detection of RNA–DNA binding sites in long noncoding RNAs
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Page e32, https://doi.org/10.1093/nar/gkz037
SpyCLIP: an easy-to-use and high-throughput compatible CLIP platform for the characterization of protein–RNA interactions with high accuracy
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Page e33, https://doi.org/10.1093/nar/gkz049
SAMURAI (Solid-phase Assisted Mutagenesis by Uracil Restriction for Accurate Integration) for antibody affinity maturation and paratope mapping
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Page e34, https://doi.org/10.1093/nar/gkz050
High resolution discovery of chromatin interactions
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Page e35, https://doi.org/10.1093/nar/gkz051
DeepRibo: a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patterns
Nucleic Acids Research, Volume 47, Issue 6, 08 April 2019, Page e36, https://doi.org/10.1093/nar/gkz061
