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Volume 41, Issue 12, 1 July 2013
Computational Biology
The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 5965–5977, https://doi.org/10.1093/nar/gkt308
RNAlyzer—novel approach for quality analysis of RNA structural models
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 5978–5990, https://doi.org/10.1093/nar/gkt318
Gene Regulation, Chromatin and Epigenetics
Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2-binding motif in chimp and human, which enables the detection of evolutionarily novel targets
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 5991–6004, https://doi.org/10.1093/nar/gkt259
Megakaryocytic leukemia 1 (MKL1) ties the epigenetic machinery to hypoxia-induced transactivation of endothelin-1
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6005–6017, https://doi.org/10.1093/nar/gkt311
MYCN and HDAC2 cooperate to repress miR-183 signaling in neuroblastoma
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6018–6033, https://doi.org/10.1093/nar/gkt346
Small molecule induced reactivation of mutant p53 in cancer cells
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6034–6044, https://doi.org/10.1093/nar/gkt305
A bistable hysteretic switch in an activator–repressor regulated restriction–modification system
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6045–6057, https://doi.org/10.1093/nar/gkt324
Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6058–6071, https://doi.org/10.1093/nar/gkt325
Progesterone receptor induces bcl-x expression through intragenic binding sites favoring RNA polymerase II elongation
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6072–6086, https://doi.org/10.1093/nar/gkt327
Repression of class I transcription by cadmium is mediated by the protein phosphatase 2A
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6087–6097, https://doi.org/10.1093/nar/gkt335
Genome Integrity, Repair and Replication
The 26S proteasome drives trinucleotide repeat expansions
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6098–6108, https://doi.org/10.1093/nar/gkt295
Clustered DNA damage induces pan-nuclear H2AX phosphorylation mediated by ATM and DNA–PK
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6109–6118, https://doi.org/10.1093/nar/gkt304
Genomics
Single-cell paired-end genome sequencing reveals structural variation per cell cycle
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6119–6138, https://doi.org/10.1093/nar/gkt345
Molecular Biology
APOBEC3G cytosine deamination hotspots are defined by both sequence context and single-stranded DNA secondary structure
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6139–6148, https://doi.org/10.1093/nar/gkt246
The SMC1-SMC3 cohesin heterodimer structures DNA through supercoiling-dependent loop formation
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6149–6160, https://doi.org/10.1093/nar/gkt303
Glucocorticoid-mediated Period2 induction delays the phase of circadian rhythm
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6161–6174, https://doi.org/10.1093/nar/gkt307
Differential regulation by ppGpp versus pppGpp in Escherichia coli
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6175–6189, https://doi.org/10.1093/nar/gkt302
Nucleic Acid Enzymes
The tRNA-modifying function of MnmE is controlled by post-hydrolysis steps of its GTPase cycle
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6190–6208, https://doi.org/10.1093/nar/gkt320
RNA
Molecular basis for improved gene silencing by Dicer substrate interfering RNA compared with other siRNA variants
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6209–6221, https://doi.org/10.1093/nar/gkt200
Stability of RNA quadruplex in open reading frame determines proteolysis of human estrogen receptor α
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6222–6231, https://doi.org/10.1093/nar/gkt286
Arabidopsis thaliana LSM proteins function in mRNA splicing and degradation
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6232–6249, https://doi.org/10.1093/nar/gkt296
RNA-Seq analyses reveal the order of tRNA processing events and the maturation of C/D box and CRISPR RNAs in the hyperthermophile Methanopyrus kandleri
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6250–6258, https://doi.org/10.1093/nar/gkt317
Recognition of two distinct elements in the RNA substrate by the RNA-binding domain of the T. thermophilus DEAD box helicase Hera
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6259–6272, https://doi.org/10.1093/nar/gkt323
Transient RNA structure features are evolutionarily conserved and can be computationally predicted
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6273–6285, https://doi.org/10.1093/nar/gkt319
The DEAD-box helicase DDX3 substitutes for the cap-binding protein eIF4E to promote compartmentalized translation initiation of the HIV-1 genomic RNA
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6286–6299, https://doi.org/10.1093/nar/gkt306
Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6300–6315, https://doi.org/10.1093/nar/gkt316
Influence of genome-scale RNA structure disruption on the replication of murine norovirus—similar replication kinetics in cell culture but attenuation of viral fitness in vivo
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6316–6331, https://doi.org/10.1093/nar/gkt334
Structural Biology
Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6332–6346, https://doi.org/10.1093/nar/gkt322
Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6347–6359, https://doi.org/10.1093/nar/gkt315
Synthetic Biology and Chemistry
Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Pages 6360–6369, https://doi.org/10.1093/nar/gkt312
Corrigendum
An efficient method for genome-wide polyadenylation site mapping and RNA quantification
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Page 6370, https://doi.org/10.1093/nar/gkt364
Methods Online
Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Page e121, https://doi.org/10.1093/nar/gkt263
Massive functional mapping of a 5′-UTR by saturation mutagenesis, phenotypic sorting and deep sequencing
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Page e122, https://doi.org/10.1093/nar/gkt267
New synthetic substrates of mammalian nucleotide excision repair system
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Page e123, https://doi.org/10.1093/nar/gkt301
Multi-chromatic control of mammalian gene expression and signaling
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Page e124, https://doi.org/10.1093/nar/gkt340
Efficient Flp-Int HK022 dual RMCE in mammalian cells
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Page e125, https://doi.org/10.1093/nar/gkt341
Synthesis of 18O-labeled RNA for application to kinetic studies and imaging
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Page e126, https://doi.org/10.1093/nar/gkt344
Monitoring eukaryotic and bacterial UDG repair activity with DNA-multifluorophore sensors
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Page e127, https://doi.org/10.1093/nar/gkt309
Reprever: resolving low-copy duplicated sequences using template driven assembly
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Page e128, https://doi.org/10.1093/nar/gkt339
Front-Matter/Back-Matter
Nucleic Acids Research: VOLUME 41 ISSUE 12 2013
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Page i, https://doi.org/10.1093/nar/gks1369
Nucleic Acids Research - Editorial Board
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Page ii, https://doi.org/10.1093/nar/gks1393
Subscriptions
Nucleic Acids Research, Volume 41, Issue 12, 1 July 2013, Page iii, https://doi.org/10.1093/nar/gks1417
