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Volume 42, Issue 4, 1 February 2014
Survey and Summary
Protein–DNA binding: complexities and multi-protein codes
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2099–2111, https://doi.org/10.1093/nar/gkt1112
Molecular recognition by the KIX domain and its role in gene regulation
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2112–2125, https://doi.org/10.1093/nar/gkt1147
Computational Biology
chroGPS, a global chromatin positioning system for the functional analysis and visualization of the epigenome
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2126–2137, https://doi.org/10.1093/nar/gkt1186
Structural determinants of DNA recognition by plant MADS-domain transcription factors
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2138–2146, https://doi.org/10.1093/nar/gkt1172
Quantifying the role of steric constraints in nucleosome positioning
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2147–2158, https://doi.org/10.1093/nar/gkt1239
Structure-based model for light-harvesting properties of nucleic acid nanostructures
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2159–2170, https://doi.org/10.1093/nar/gkt1269
Gene Regulation, Chromatin and Epigenetics
Transcription factor abundance controlled by an auto-regulatory mechanism involving a transcription start site switch
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2171–2184, https://doi.org/10.1093/nar/gkt1136
The chromatin remodeller CHD8 is required for E2F-dependent transcription activation of S-phase genes
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2185–2196, https://doi.org/10.1093/nar/gkt1161
The Ddx5 and Ddx17 RNA helicases are cornerstones in the complex regulatory array of steroid hormone-signaling pathways
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2197–2207, https://doi.org/10.1093/nar/gkt1216
YY1 DNA binding and interaction with YAF2 is essential for Polycomb recruitment
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2208–2223, https://doi.org/10.1093/nar/gkt1187
Discrimination between thermodynamic models of cis-regulation using transcription factor occupancy data
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2224–2234, https://doi.org/10.1093/nar/gkt1230
Collaboration between CpG sites is needed for stable somatic inheritance of DNA methylation states
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2235–2244, https://doi.org/10.1093/nar/gkt1235
Establishment of active chromatin structure at enhancer elements by mixed-lineage leukemia 1 to initiate estrogen-dependent gene expression
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2245–2256, https://doi.org/10.1093/nar/gkt1236
Genome Integrity, Repair and Replication
The ORC/Cdc6/MCM2-7 complex facilitates MCM2-7 dimerization during prereplicative complex formation
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2257–2269, https://doi.org/10.1093/nar/gkt1148
DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2270–2281, https://doi.org/10.1093/nar/gkt1174
Multiple replication origins with diverse control mechanisms in Haloarcula hispanica
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2282–2294, https://doi.org/10.1093/nar/gkt1214
Bacillus subtilis RecA and its accessory factors, RecF, RecO, RecR and RecX, are required for spore resistance to DNA double-strand break
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2295–2307, https://doi.org/10.1093/nar/gkt1194
DNA binding properties of human Cdc45 suggest a function as molecular wedge for DNA unwinding
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2308–2319, https://doi.org/10.1093/nar/gkt1217
ARF induction in response to DNA strand breaks is regulated by PARP1
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2320–2329, https://doi.org/10.1093/nar/gkt1185
Novel method for site-specific induction of oxidative DNA damage reveals differences in recruitment of repair proteins to heterochromatin and euchromatin
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2330–2345, https://doi.org/10.1093/nar/gkt1233
The dual role of HOP2 in mammalian meiotic homologous recombination
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2346–2357, https://doi.org/10.1093/nar/gkt1234
Swi5-Sfr1 protein stimulates Rad51-mediated DNA strand exchange reaction through organization of DNA bases in the presynaptic filament
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2358–2365, https://doi.org/10.1093/nar/gkt1257
Identification of genes involved in low aminoglycoside-induced SOS response in Vibrio cholerae: a role for transcription stalling and Mfd helicase
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2366–2379, https://doi.org/10.1093/nar/gkt1259
Human RECQ5 helicase promotes repair of DNA double-strand breaks by synthesis-dependent strand annealing
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2380–2390, https://doi.org/10.1093/nar/gkt1263
Genomics
Phylo SI: a new genome-wide approach for prokaryotic phylogeny
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2391–2404, https://doi.org/10.1093/nar/gkt1138
Genetic robustness and functional evolution of gene duplicates
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2405–2414, https://doi.org/10.1093/nar/gkt1200
The complex methylome of the human gastric pathogen Helicobacter pylori
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2415–2432, https://doi.org/10.1093/nar/gkt1201
Vespucci: a system for building annotated databases of nascent transcripts
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2433–2447, https://doi.org/10.1093/nar/gkt1237
Expanding the catalog of cas genes with metagenomes
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2448–2459, https://doi.org/10.1093/nar/gkt1262
Molecular Biology
Dual role of transcription and transcript stability in the regulation of gene expression in Escherichia coli cells cultured on glucose at different growth rates
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2460–2472, https://doi.org/10.1093/nar/gkt1150
Modification of picornavirus genomic RNA using ‘click’ chemistry shows that unlinking of the VPg peptide is dispensable for translation and replication of the incoming viral RNA
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2473–2482, https://doi.org/10.1093/nar/gkt1162
Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2483–2492, https://doi.org/10.1093/nar/gkt1154
TRF1 and TRF2 use different mechanisms to find telomeric DNA but share a novel mechanism to search for protein partners at telomeres
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2493–2504, https://doi.org/10.1093/nar/gkt1132
Back to translation: removal of aIF2 from the 5′-end of mRNAs by translation recovery factor in the crenarchaeon Sulfolobus solfataricus
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2505–2511, https://doi.org/10.1093/nar/gkt1169
Spatio-temporal requirements for transposable element piRNA-mediated silencing during Drosophila oogenesis
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2512–2524, https://doi.org/10.1093/nar/gkt1184
Differential contribution of basic residues to HIV-1 nucleocapsid protein’s nucleic acid chaperone function and retroviral replication
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2525–2537, https://doi.org/10.1093/nar/gkt1227
A cypovirus VP5 displays the RNA chaperone-like activity that destabilizes RNA helices and accelerates strand annealing
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2538–2554, https://doi.org/10.1093/nar/gkt1256
Nucleic Acid Enzymes
Nucleotide selection by the Y-family DNA polymerase Dpo4 involves template translocation and misalignment
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2555–2563, https://doi.org/10.1093/nar/gkt1149
Reprogramming homing endonuclease specificity through computational design and directed evolution
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2564–2576, https://doi.org/10.1093/nar/gkt1212
Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2577–2590, https://doi.org/10.1093/nar/gkt1074
megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2591–2601, https://doi.org/10.1093/nar/gkt1224
The output of the tRNA modification pathways controlled by the Escherichia coli MnmEG and MnmC enzymes depends on the growth conditions and the tRNA species
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2602–2623, https://doi.org/10.1093/nar/gkt1228
Structure and DNA-binding properties of the Bacillus subtilis SpoIIIE DNA translocase revealed by single-molecule and electron microscopies
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2624–2636, https://doi.org/10.1093/nar/gkt1231
Hyperactive mariner transposons are created by mutations that disrupt allosterism and increase the rate of transposon end synapsis
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2637–2645, https://doi.org/10.1093/nar/gkt1218
RNA
Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2646–2659, https://doi.org/10.1093/nar/gkt1139
Trans-splicing and RNA editing of LSU rRNA in Diplonema mitochondria
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2660–2672, https://doi.org/10.1093/nar/gkt1152
Structural and functional analysis of the three MIF4G domains of nonsense-mediated decay factor UPF2
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2673–2686, https://doi.org/10.1093/nar/gkt1197
Differences between cotranscriptional and free riboswitch folding
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2687–2696, https://doi.org/10.1093/nar/gkt1213
Poly(A) RNA and Paip2 act as allosteric regulators of poly(A)-binding protein
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2697–2707, https://doi.org/10.1093/nar/gkt1170
Identification of truncated forms of U1 snRNA reveals a novel RNA degradation pathway during snRNP biogenesis
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2708–2724, https://doi.org/10.1093/nar/gkt1271
Structural Biology
Structural insight into DNA binding and oligomerization of the multifunctional Cox protein of bacteriophage P2
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2725–2735, https://doi.org/10.1093/nar/gkt1119
Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2736–2749, https://doi.org/10.1093/nar/gkt1171
Intramolecular binding mode of the C-terminus of Escherichia coli single-stranded DNA binding protein determined by nuclear magnetic resonance spectroscopy
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2750–2757, https://doi.org/10.1093/nar/gkt1238
RNA-dependent RNA polymerase of Japanese encephalitis virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2758–2773, https://doi.org/10.1093/nar/gkt1106
Structural mechanism of transcription regulation of the Staphylococcus aureus multidrug efflux operon mepRA by the MarR family repressor MepR
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2774–2788, https://doi.org/10.1093/nar/gkt1215
Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Pages 2789–2797, https://doi.org/10.1093/nar/gkt1219
Corrigendum
Interplay between REST and nucleolin transcription factors: a key mechanism in the overexpression of genes upon increased phosphorylation
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Page 2798, https://doi.org/10.1093/nar/gkt1283
Methods Online
High-throughput, cost-effective verification of structural DNA assembly
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Page e22, https://doi.org/10.1093/nar/gkt1088
Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Page e23, https://doi.org/10.1093/nar/gkt1101
Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Page e24, https://doi.org/10.1093/nar/gkt1105
UnSplicer: mapping spliced RNA-seq reads in compact genomes and filtering noisy splicing
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Page e25, https://doi.org/10.1093/nar/gkt1141
One-step zero-background IgG reformatting of phage-displayed antibody fragments enabling rapid and high-throughput lead identification
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Page e26, https://doi.org/10.1093/nar/gkt1142
Method for site-specific detection of m6A nucleoside presence in RNA based on high-resolution melting (HRM) analysis
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Page e27, https://doi.org/10.1093/nar/gkt1160
DNA transposition by protein transduction of the piggyBac transposase from lentiviral Gag precursors
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Page e28, https://doi.org/10.1093/nar/gkt1163
Highly specific and sensitive method for measuring nucleotide excision repair kinetics of ultraviolet photoproducts in human cells
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Page e29, https://doi.org/10.1093/nar/gkt1179
Front-Matter/Back-Matter
Nucleic Acids Research: VOLUME 42 ISSUE 4 2014
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Page i, https://doi.org/10.1093/nar/gku016
Nucleic Acids Research - Editorial Board
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Page ii, https://doi.org/10.1093/nar/gku039
Subscriptions
Nucleic Acids Research, Volume 42, Issue 4, 1 February 2014, Page iii, https://doi.org/10.1093/nar/gku062
