Volume 44, Issue 21
December 2016
Cover image
Cover image
Cover: Model for negative DNA supercoiling by gyrase with one catalytic tyrosine after a nicking-closing mechanism. Gyrase captures two positive supercoils (2 +sc) on the DNA substrate, which leads to the formation of compensatory negative supercoils (2 −sc) elsewhere. Wrapping of the DNA around the CTD and single-strand cleavage lead to separation of these topological domains. ATP binding then induces release of the wrap, freeing one end of the topological domain with the positive supercoils, and allowing for their relaxation. Religation of the nicked strand fixes the change in linking number by −2.
For more information see article by Gubaev, A. et al., pages 10354–10366 in this issue.
For more information see article by Gubaev, A. et al., pages 10354–10366 in this issue.
ISSN 0305-1048
EISSN 1362-4962
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Volume 44, Issue 21, December 2016
Survey and Summary
The multifaceted influence of histone deacetylases on DNA damage signalling and DNA repair
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10017–10030, https://doi.org/10.1093/nar/gkw922
Chemical Biology and Nucleic Acid Chemistry
Light-induced oxidation of the telomeric G4 DNA in complex with Zn(II) tetracarboxymethyl porphyrin
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10031–10041, https://doi.org/10.1093/nar/gkw947
Modification of orthogonal tRNAs: unexpected consequences for sense codon reassignment
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10042–10050, https://doi.org/10.1093/nar/gkw948
Computational Biology
Codon usage is less optimized in eukaryotic gene segments encoding intrinsically disordered regions than in those encoding structural domains
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10051–10061, https://doi.org/10.1093/nar/gkw899
Localized structural frustration for evaluating the impact of sequence variants
Nucleic Acids Research, Volume 44, Issue 21, December 2016, gkw927, https://doi.org/10.1093/nar/gkw927
Data Resources and Analyses
The landscape of microbial phenotypic traits and associated genes
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10074–10090, https://doi.org/10.1093/nar/gkw964
Gene Regulation, Chromatin and Epigenetics
Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10091–10105, https://doi.org/10.1093/nar/gkw684
Evaluating the impact of single nucleotide variants on transcription factor binding
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10106–10116, https://doi.org/10.1093/nar/gkw691
Silencing of cryptic prophages in Corynebacterium glutamicum
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10117–10131, https://doi.org/10.1093/nar/gkw692
Interdependence of PRC1 and PRC2 for recruitment to Polycomb Response Elements
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10132–10149, https://doi.org/10.1093/nar/gkw701
Genome-wide co-localization of active EGFR and downstream ERK pathway kinases mirrors mitogen-inducible RNA polymerase 2 genomic occupancy
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10150–10164, https://doi.org/10.1093/nar/gkw763
Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10165–10176, https://doi.org/10.1093/nar/gkw766
Distinctive Klf4 mutants determine preference for DNA methylation status
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10177–10185, https://doi.org/10.1093/nar/gkw774
Insights into the regulation of small RNA expression: SarA represses the expression of two sRNAs in Staphylococcus aureus
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10186–10200, https://doi.org/10.1093/nar/gkw777
Genome Integrity, Repair and Replication
Novel TDP2-ubiquitin interactions and their importance for the repair of topoisomerase II-mediated DNA damage
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10201–10215, https://doi.org/10.1093/nar/gkw719
Incision of damaged DNA in the presence of an impaired Smc5/6 complex imperils genome stability
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10216–10229, https://doi.org/10.1093/nar/gkw720
Genome-wide identification and characterisation of human DNA replication origins by initiation site sequencing (ini-seq)
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10230–10247, https://doi.org/10.1093/nar/gkw760
Structural basis of damage recognition by thymine DNA glycosylase: Key roles for N-terminal residues
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10248–10258, https://doi.org/10.1093/nar/gkw768
DNA damage response curtails detrimental replication stress and chromosomal instability induced by the dietary carcinogen PhIP
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10259–10276, https://doi.org/10.1093/nar/gkw791
Genomics
Differential cytokine sensitivities of STAT5-dependent enhancers rely on Stat5 autoregulation
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10277–10291, https://doi.org/10.1093/nar/gkw844
Molecular Biology
Global tRNA misacylation induced by anaerobiosis and antibiotic exposure broadly increases stress resistance in Escherichia coli
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10292–10303, https://doi.org/10.1093/nar/gkw856
Single-molecule FRET reveals the pre-initiation and initiation conformations of influenza virus promoter RNA
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10304–10315, https://doi.org/10.1093/nar/gkw884
The dual role of DksA protein in the regulation of Escherichia coli pArgX promoter
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10316–10325, https://doi.org/10.1093/nar/gkw912
Mechanistic determinants of MBNL activity
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10326–10342, https://doi.org/10.1093/nar/gkw915
Visualization of DNA G-quadruplexes in herpes simplex virus 1-infected cells
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10343–10353, https://doi.org/10.1093/nar/gkw968
Nucleic Acid Enzymes
DNA gyrase with a single catalytic tyrosine can catalyze DNA supercoiling by a nicking-closing mechanism
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10354–10366, https://doi.org/10.1093/nar/gkw740
Casposon integration shows strong target site preference and recapitulates protospacer integration by CRISPR-Cas systems
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10367–10376, https://doi.org/10.1093/nar/gkw821
A highly specific sodium aptamer probed by 2-aminopurine for robust Na+ sensing
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10377–10385, https://doi.org/10.1093/nar/gkw845
Analyzing structure–function relationships of artificial and cancer-associated PARP1 variants by reconstituting TALEN-generated HeLa PARP1 knock-out cells
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10386–10405, https://doi.org/10.1093/nar/gkw859
RNA
The target spectrum of SdsR small RNA in Salmonella
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10406–10422, https://doi.org/10.1093/nar/gkw632
Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10423–10436, https://doi.org/10.1093/nar/gkw637
Perlman syndrome nuclease DIS3L2 controls cytoplasmic non-coding RNAs and provides surveillance pathway for maturing snRNAs
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10437–10453, https://doi.org/10.1093/nar/gkw649
Cytoplasmic Drosha activity generated by alternative splicing
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10454–10466, https://doi.org/10.1093/nar/gkw668
Structural Biology
Dynamic peptides of human TPP1 fulfill diverse functions in telomere maintenance
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10467–10479, https://doi.org/10.1093/nar/gkw846
Crystal structure of endonuclease G in complex with DNA reveals how it nonspecifically degrades DNA as a homodimer
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10480–10490, https://doi.org/10.1093/nar/gkw931
Structure of the 70S ribosome from human pathogen Staphylococcus aureus
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10491–10504, https://doi.org/10.1093/nar/gkw933
Molecular mechanism of divalent-metal-induced activation of NS3 helicase and insights into Zika virus inhibitor design
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10505–10514, https://doi.org/10.1093/nar/gkw941
Synthetic Biology and Bioengineering
Insightful directed evolution of Escherichia coli quorum sensing promoter region of the lsrACDBFG operon: a tool for synthetic biology systems and protein expression
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Pages 10515–10525, https://doi.org/10.1093/nar/gkw981
Corrigendum
A fast and powerful W-test for pairwise epistasis testing
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Page 10526, https://doi.org/10.1093/nar/gkw866
Methods Online
Analysis of C. elegans muscle transcriptome using trans-splicing-based RNA tagging (SRT)
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Page e156, https://doi.org/10.1093/nar/gkw734
An efficient system for selectively altering genetic information within mRNAs
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Page e157, https://doi.org/10.1093/nar/gkw738
Single-nucleus RNA-seq of differentiating human myoblasts reveals the extent of fate heterogeneity
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Page e158, https://doi.org/10.1093/nar/gkw739
PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Page e159, https://doi.org/10.1093/nar/gkw741
Single molecule tracking of Ace1p in Saccharomyces cerevisiae defines a characteristic residence time for non-specific interactions of transcription factors with chromatin
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Page e160, https://doi.org/10.1093/nar/gkw744
Front-Matter/Back-Matter
Nucleic Acids Research: VOLUME 44 ISSUE 21 2016
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Page i, https://doi.org/10.1093/nar/gkv1426
Nucleic Acids Research: Editorial Board
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Page ii, https://doi.org/10.1093/nar/gkv1424
Subscriptions
Nucleic Acids Research, Volume 44, Issue 21, December 2016, Page iii, https://doi.org/10.1093/nar/gkv1425
