Volume 45, Issue 9
19 May 2017
Cover image
Cover image
Cover: The many structures of single stranded DNA, dA30 in this case, revealed by experimentally validated ensemble optimization. This method can be applied to identify ensembles of highly flexible structures of arbitrary length and sequence.
For more information see article by Plumridge, A. et al., pages e66 in this issue.
For more information see article by Plumridge, A. et al., pages e66 in this issue.
ISSN 0305-1048
EISSN 1362-4962
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Volume 45, Issue 9, 19 May 2017
NAR Breakthrough Article
The CDI toxin of Yersinia kristensenii is a novel bacterial member of the RNase A superfamily
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5013–5025, https://doi.org/10.1093/nar/gkx230
Chemical Biology and Nucleic Acid Chemistry
Chiral metallohelices enantioselectively target hybrid human telomeric G-quadruplex DNA
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5026–5035, https://doi.org/10.1093/nar/gkx244
Pseudorotaxane formation via the slippage process with chemically cyclized oligonucleotides
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5036–5047, https://doi.org/10.1093/nar/gkx265
Computational Biology
Enhancing identification of cancer types via lowly-expressed microRNAs
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5048–5060, https://doi.org/10.1093/nar/gkx210
Data Resources and Analyses
A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5061–5073, https://doi.org/10.1093/nar/gkx267
Gene Regulation, Chromatin and Epigenetics
Efficient chromosomal-scale DNA looping in Escherichia coli using multiple DNA-looping elements
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5074–5085, https://doi.org/10.1093/nar/gkx069
p27Kip1, PCAF and PAX5 cooperate in the transcriptional regulation of specific target genes
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5086–5099, https://doi.org/10.1093/nar/gkx075
Modeling complex patterns of differential DNA methylation that associate with gene expression changes
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5100–5111, https://doi.org/10.1093/nar/gkx078
Homo-trimerization is essential for the transcription factor function of Myrf for oligodendrocyte differentiation
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5112–5125, https://doi.org/10.1093/nar/gkx080
Natural antisense transcripts are significantly involved in regulation of drought stress in maize
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5126–5141, https://doi.org/10.1093/nar/gkx085
tRNA-derived small RNAs target transposable element transcripts
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5142–5152, https://doi.org/10.1093/nar/gkx103
CTG repeat-targeting oligonucleotides for down-regulating Huntingtin expression
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5153–5169, https://doi.org/10.1093/nar/gkx111
TIEG1 modulates β-catenin sub-cellular localization and enhances Wnt signaling in bone
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5170–5182, https://doi.org/10.1093/nar/gkx118
Gcn5-mediated Rph1 acetylation regulates its autophagic degradation under DNA damage stress
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5183–5197, https://doi.org/10.1093/nar/gkx129
Genome Integrity, Repair and Replication
Highly efficient biallelic genome editing of human ES/iPS cells using a CRISPR/Cas9 or TALEN system
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5198–5207, https://doi.org/10.1093/nar/gkx130
High tolerance to self-targeting of the genome by the endogenous CRISPR-Cas system in an archaeon
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5208–5216, https://doi.org/10.1093/nar/gkx150
Yeast Hrq1 shares structural and functional homology with the disease-linked human RecQ4 helicase
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5217–5230, https://doi.org/10.1093/nar/gkx151
The mechanism of the glycosylase reaction with hOGG1 base-excision repair enzyme: concerted effect of Lys249 and Asp268 during excision of 8-oxoguanine
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5231–5242, https://doi.org/10.1093/nar/gkx157
Avoidance of APOBEC3B-induced mutation by error-free lesion bypass
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5243–5254, https://doi.org/10.1093/nar/gkx169
Rad50 ATPase activity is regulated by DNA ends and requires coordination of both active sites
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5255–5268, https://doi.org/10.1093/nar/gkx173
Rgf1p (Rho1p GEF) is required for double-strand break repair in fission yeast
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5269–5284, https://doi.org/10.1093/nar/gkx176
Genomics
Genomic and transcriptomic landscape of Escherichia coli BL21(DE3)
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5285–5293, https://doi.org/10.1093/nar/gkx228
Molecular Biology
Truncated ORF1 proteins can suppress LINE-1 retrotransposition in trans
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5294–5308, https://doi.org/10.1093/nar/gkx211
Intra-endosomal trafficking mediated by lysobisphosphatidic acid contributes to intracellular release of phosphorothioate-modified antisense oligonucleotides
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5309–5322, https://doi.org/10.1093/nar/gkx231
Nucleic Acid Enzymes
High pressure activation of the Mrr restriction endonuclease in Escherichia coli involves tetramer dissociation
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5323–5332, https://doi.org/10.1093/nar/gkx192
Substrate preference of Gen endonucleases highlights the importance of branched structures as DNA damage repair intermediates
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5333–5348, https://doi.org/10.1093/nar/gkx214
Deacetylation of topoisomerase I is an important physiological function of E. coli CobB
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5349–5358, https://doi.org/10.1093/nar/gkx250
RNA
The G-patch protein NF-κB-repressing factor mediates the recruitment of the exonuclease XRN2 and activation of the RNA helicase DHX15 in human ribosome biogenesis
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5359–5374, https://doi.org/10.1093/nar/gkx013
Ligand binding to 2΄-deoxyguanosine sensing riboswitch in metabolic context
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5375–5386, https://doi.org/10.1093/nar/gkx016
Roles of MIWI, MILI and PLD6 in small RNA regulation in mouse growing oocytes
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5387–5398, https://doi.org/10.1093/nar/gkx027
SECIS-binding protein 2 interacts with the SMN complex and the methylosome for selenoprotein mRNP assembly and translation
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5399–5413, https://doi.org/10.1093/nar/gkx031
Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5414–5422, https://doi.org/10.1093/nar/gkx045
Human BCDIN3D monomethylates cytoplasmic histidine transfer RNA
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5423–5436, https://doi.org/10.1093/nar/gkx051
Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5437–5448, https://doi.org/10.1093/nar/gkx061
Self-assembly of multi-stranded RNA motifs into lattices and tubular structures
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5449–5457, https://doi.org/10.1093/nar/gkx063
The lncRNA VELUCT strongly regulates viability of lung cancer cells despite its extremely low abundance
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5458–5469, https://doi.org/10.1093/nar/gkx076
A transposon-derived small RNA regulates gene expression in Salmonella Typhimurium
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5470–5486, https://doi.org/10.1093/nar/gkx094
Simultaneous processing and degradation of mitochondrial RNAs revealed by circularized RNA sequencing
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5487–5500, https://doi.org/10.1093/nar/gkx104
Characterization of human telomere RNA G-quadruplex structures in vitro and in living cells using 19F NMR spectroscopy
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5501–5511, https://doi.org/10.1093/nar/gkx109
Ligand-modulated folding of the full-length adenine riboswitch probed by NMR and single-molecule FRET spectroscopy
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5512–5522, https://doi.org/10.1093/nar/gkx110
Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5523–5538, https://doi.org/10.1093/nar/gkx115
A single miR390 targeting event is sufficient for triggering TAS3-tasiRNA biogenesis in Arabidopsis
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5539–5554, https://doi.org/10.1093/nar/gkx119
Structural Biology
Crystal structure of the N-terminal domain of human Timeless and its interaction with Tipin
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5555–5563, https://doi.org/10.1093/nar/gkx139
Structural characterization of interactions between transactivation domain 1 of the p65 subunit of NF-κB and transcription regulatory factors
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5564–5576, https://doi.org/10.1093/nar/gkx146
Structure of the Sac3 RNA-binding M-region in the Saccharomyces cerevisiae TREX-2 complex
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5577–5585, https://doi.org/10.1093/nar/gkx158
Insights into Watson–Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5586–5601, https://doi.org/10.1093/nar/gkx186
NMR-based method of small changes reveals how DNA mutator APOBEC3A interacts with its single-stranded DNA substrate
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5602–5613, https://doi.org/10.1093/nar/gkx196
Synthetic Biology and Bioengineering
Achieving large dynamic range control of gene expression with a compact RNA transcription–translation regulator
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5614–5624, https://doi.org/10.1093/nar/gkx215
Corrigendum
ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Pages 5625–5626, https://doi.org/10.1093/nar/gkw1342
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Page 5627, https://doi.org/10.1093/nar/gkx021
Self-assembly of multi-stranded RNA motifs into lattices and tubular structures
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Page 5628, https://doi.org/10.1093/nar/gkx227
Methods Online
Visualizing single-stranded nucleic acids in solution
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Page e66, https://doi.org/10.1093/nar/gkw1297
PBrowse: a web-based platform for real-time collaborative exploration of genomic data
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Page e67, https://doi.org/10.1093/nar/gkw1358
Amplification of unscheduled DNA synthesis signal enables fluorescence-based single cell quantification of transcription-coupled nucleotide excision repair
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Page e68, https://doi.org/10.1093/nar/gkw1360
Computational approach for deriving cancer progression roadmaps from static sample data
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Page e69, https://doi.org/10.1093/nar/gkx003
YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Page e70, https://doi.org/10.1093/nar/gkx005
From benchmarking HITS-CLIP peak detection programs to a new method for identification of miRNA-binding sites from Ago2-CLIP data
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Page e71, https://doi.org/10.1093/nar/gkx007
digit—a tool for detection and identification of genomic interchromosomal translocations
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Page e72, https://doi.org/10.1093/nar/gkx010
High-throughput single-molecule mapping links subtelomeric variants and long-range haplotypes with specific telomeres
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Page e73, https://doi.org/10.1093/nar/gkx017
The CCTL (Cpf1-assisted Cutting and Taq DNA ligase-assisted Ligation) method for efficient editing of large DNA constructs in vitro
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Page e74, https://doi.org/10.1093/nar/gkx018
Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework
Nucleic Acids Research, Volume 45, Issue 9, 19 May 2017, Page e75, https://doi.org/10.1093/nar/gkx019
