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Volume 41, Issue 5, 1 March 2013
Survey and Summaries
Physico-chemical foundations underpinning microarray and next-generation sequencing experiments
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 2779–2796, https://doi.org/10.1093/nar/gks1358
Histone H4 Lysine 20 methylation: key player in epigenetic regulation of genomic integrity
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 2797–2806, https://doi.org/10.1093/nar/gkt012
Computational Biology
Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 2807–2816, https://doi.org/10.1093/nar/gks1283
Interplay of microRNAs, transcription factors and target genes: linking dynamic expression changes to function
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 2817–2831, https://doi.org/10.1093/nar/gks1471
Evolutionary history of the TBP-domain superfamily
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 2832–2845, https://doi.org/10.1093/nar/gkt045
Gene Regulation, Chromatin and Epigenetics
Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 2846–2856, https://doi.org/10.1093/nar/gks1336
Nucleosome mapping across the CFTR locus identifies novel regulatory factors
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 2857–2868, https://doi.org/10.1093/nar/gks1462
Nap1 regulates proper CENP-B binding to nucleosomes
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 2869–2880, https://doi.org/10.1093/nar/gks1464
Histone methyltransferase SETD2 coordinates FACT recruitment with nucleosome dynamics during transcription
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 2881–2893, https://doi.org/10.1093/nar/gks1472
An autonomous chromatin/DNA-PK mechanism for localized DNA damage signaling in mammalian cells
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 2894–2906, https://doi.org/10.1093/nar/gks1478
Dual function of MIPS1 as a metabolic enzyme and transcriptional regulator
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 2907–2917, https://doi.org/10.1093/nar/gks1458
Effects of DNA methylation on nucleosome stability
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 2918–2931, https://doi.org/10.1093/nar/gks893
Expanded target and cofactor repertoire for the transcriptional activator LysM from Sulfolobus
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 2932–2949, https://doi.org/10.1093/nar/gkt021
The Epstein–Barr virus nuclear antigen-1 reprograms transcription by mimicry of high mobility group A proteins
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 2950–2962, https://doi.org/10.1093/nar/gkt032
Genome-wide localization of exosome components to active promoters and chromatin insulators in Drosophila
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 2963–2980, https://doi.org/10.1093/nar/gkt037
TDP1 is an HMG chromatin protein facilitating RNA polymerase I transcription in African trypanosomes
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 2981–2992, https://doi.org/10.1093/nar/gks1469
Epigenetic diversity of Kaposi’s sarcoma–associated herpesvirus
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 2993–3009, https://doi.org/10.1093/nar/gkt033
Differential roles for MBD2 and MBD3 at methylated CpG islands, active promoters and binding to exon sequences
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3010–3021, https://doi.org/10.1093/nar/gkt035
Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3022–3031, https://doi.org/10.1093/nar/gkt057
Genome Integrity, Repair and Replication
MSH6- or PMS2-deficiency causes re-replication in DT40 B cells, but it has little effect on immunoglobulin gene conversion or on repair of AID-generated uracils
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3032–3046, https://doi.org/10.1093/nar/gks1470
The nitrosated bile acid DNA lesion O6 -carboxymethylguanine is a substrate for the human DNA repair protein O6 -methylguanine-DNA methyltransferase
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3047–3055, https://doi.org/10.1093/nar/gks1476
Spontaneous telomere to telomere fusions occur in unperturbed fission yeast cells
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3056–3067, https://doi.org/10.1093/nar/gks1459
Prevalent coordination of mitochondrial DNA transcription and initiation of replication with the cell cycle
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3068–3078, https://doi.org/10.1093/nar/gkt015
A non-catalytic role of DNA polymerase η in recruiting Rad18 and promoting PCNA monoubiquitination at stalled replication forks
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3079–3093, https://doi.org/10.1093/nar/gkt016
Insight into centromere-binding properties of ParB proteins: a secondary binding motif is essential for bacterial genome maintenance
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3094–3103, https://doi.org/10.1093/nar/gkt018
UV damage regulates alternative polyadenylation of the RPB2 gene in yeast
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3104–3114, https://doi.org/10.1093/nar/gkt020
Distinct spatiotemporal patterns and PARP dependence of XRCC1 recruitment to single-strand break and base excision repair
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3115–3129, https://doi.org/10.1093/nar/gkt025
RNase H2 roles in genome integrity revealed by unlinking its activities
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3130–3143, https://doi.org/10.1093/nar/gkt027
Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3144–3161, https://doi.org/10.1093/nar/gkt029
In the absence of ATPase activity, pre-RC formation is blocked prior to MCM2–7 hexamer dimerization
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3162–3172, https://doi.org/10.1093/nar/gkt043
MRX protects fork integrity at protein–DNA barriers, and its absence causes checkpoint activation dependent on chromatin context
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3173–3189, https://doi.org/10.1093/nar/gkt051
Genomics
Turning gold into ‘junk’: transposable elements utilize central proteins of cellular networks
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3190–3200, https://doi.org/10.1093/nar/gkt011
Hyper conserved elements in vertebrate mRNA 3′-UTRs reveal a translational network of RNA-binding proteins controlled by HuR
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3201–3216, https://doi.org/10.1093/nar/gkt017
Molecular Biology
Mutational analysis of the ribosome assembly GTPase RbgA provides insight into ribosome interaction and ribosome-stimulated GTPase activation
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3217–3227, https://doi.org/10.1093/nar/gks1475
Nucleophosmin mutations alter its nucleolar localization by impairing G-quadruplex binding at ribosomal DNA
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3228–3239, https://doi.org/10.1093/nar/gkt001
CREB regulates the expression of neuronal glucose transporter 3: a possible mechanism related to impaired brain glucose uptake in Alzheimer’s disease
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3240–3256, https://doi.org/10.1093/nar/gks1227
Development of bis-locked nucleic acid (bisLNA) oligonucleotides for efficient invasion of supercoiled duplex DNA
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3257–3273, https://doi.org/10.1093/nar/gkt007
Helicobacter pylori DprA alleviates restriction barrier for incoming DNA
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3274–3288, https://doi.org/10.1093/nar/gkt024
Nucleic Acid Enzymes
Cooperative recruitment of HMGB1 during V(D)J recombination through interactions with RAG1 and DNA
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3289–3301, https://doi.org/10.1093/nar/gks1461
IS 200 /IS 605 family single-strand transposition: mechanism of IS 608 strand transfer
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3302–3313, https://doi.org/10.1093/nar/gkt014
MCPIP1 ribonuclease exhibits broad-spectrum antiviral effects through viral RNA binding and degradation
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3314–3326, https://doi.org/10.1093/nar/gkt019
Lewis acid catalysis of phosphoryl transfer from a copper(II)-NTP complex in a kinase ribozyme
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3327–3338, https://doi.org/10.1093/nar/gkt039
RNA
Deep sequencing of small RNAs identifies canonical and non-canonical miRNA and endogenous siRNAs in mammalian somatic tissues
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3339–3351, https://doi.org/10.1093/nar/gks1474
Structure, evolution and function of the bi-directionally transcribed iab-4/iab-8 microRNA locus in arthropods
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3352–3361, https://doi.org/10.1093/nar/gks1445
Importance of adenosine-to-inosine editing adjacent to the anticodon in an Arabidopsis alanine tRNA under environmental stress
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3362–3372, https://doi.org/10.1093/nar/gkt013
Molecular paleontology: a biochemical model of the ancestral ribosome
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3373–3385, https://doi.org/10.1093/nar/gkt023
Characterization of MicA interactions suggests a potential novel means of gene regulation by small non-coding RNAs
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3386–3397, https://doi.org/10.1093/nar/gkt008
Cation-dependent folding of 3′ cap-independent translation elements facilitates interaction of a 17-nucleotide conserved sequence with eIF4G
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3398–3413, https://doi.org/10.1093/nar/gkt026
Structural Biology
Mycobacterium tuberculosis RsdA provides a conformational rationale for selective regulation of σ-factor activity by proteolysis
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3414–3423, https://doi.org/10.1093/nar/gks1468
Solution properties of the archaeal CRISPR DNA repeat-binding homeodomain protein Cbp2
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3424–3435, https://doi.org/10.1093/nar/gks1465
Conformational rearrangements of RIG-I receptor on formation of a multiprotein:dsRNA assembly
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3436–3445, https://doi.org/10.1093/nar/gks1477
Mini-chromosome maintenance complexes form a filament to remodel DNA structure and topology
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3446–3456, https://doi.org/10.1093/nar/gkt022
Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9)
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3457–3470, https://doi.org/10.1093/nar/gkt042
Synthetic Biology and Chemistry
Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Pages 3471–3481, https://doi.org/10.1093/nar/gkt052
Methods Online
Nanobody®-based chromatin immunoprecipitation/micro-array analysis for genome-wide identification of transcription factor DNA binding sites
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Page e59, https://doi.org/10.1093/nar/gks1342
Improved methods for creating migratable Holliday junction substrates
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Page e60, https://doi.org/10.1093/nar/gks1343
rDNA-directed integration by an HIV-1 integrase—I-PpoI fusion protein
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Page e61, https://doi.org/10.1093/nar/gks1438
Widespread inference of weighted microRNA-mediated gene regulation in cancer transcriptome analysis
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Page e62, https://doi.org/10.1093/nar/gks1439
Differential integrity of TALE nuclease genes following adenoviral and lentiviral vector gene transfer into human cells
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Page e63, https://doi.org/10.1093/nar/gks1446
ParseCNV integrative copy number variation association software with quality tracking
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Page e64, https://doi.org/10.1093/nar/gks1346
An efficient method for genome-wide polyadenylation site mapping and RNA quantification
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Page e65, https://doi.org/10.1093/nar/gks1249
Front-Matter/Back-Matter
Nucleic Acids Research: VOLUME 41 ISSUE 5 2013
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Page i, https://doi.org/10.1093/nar/gks1383
Nucleic Acids Research - Editorial Board
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Page ii, https://doi.org/10.1093/nar/gks1407
Subscriptions
Nucleic Acids Research, Volume 41, Issue 5, 1 March 2013, Page iii, https://doi.org/10.1093/nar/gks1431
