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Volume 42, Issue 7, 1 April 2014
Computational Biology
Chromosome positioning from activity-based segregation
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4145–4159, https://doi.org/10.1093/nar/gkt1417
The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4160–4179, https://doi.org/10.1093/nar/gkt1414
Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4180–4195, https://doi.org/10.1093/nar/gkt1415
Physical constraints determine the logic of bacterial promoter architectures
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4196–4207, https://doi.org/10.1093/nar/gku078
Constructing module maps for integrated analysis of heterogeneous biological networks
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4208–4219, https://doi.org/10.1093/nar/gku102
Gene Regulation, Chromatin and Epigenetics
Suppression of intragenic transcription requires the MOT1 and NC2 regulators of TATA-binding protein
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4220–4229, https://doi.org/10.1093/nar/gkt1398
Androgen receptor uses relaxed response element stringency for selective chromatin binding and transcriptional regulation in vivo
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4230–4240, https://doi.org/10.1093/nar/gkt1401
MLL fusion proteins link transcriptional coactivators to previously active CpG-rich promoters
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4241–4256, https://doi.org/10.1093/nar/gkt1394
MLV integration site selection is driven by strong enhancers and active promoters
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4257–4269, https://doi.org/10.1093/nar/gkt1399
The RSC chromatin remodeling complex has a crucial role in the complete remodeler set for yeast PHO5 promoter opening
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4270–4282, https://doi.org/10.1093/nar/gkt1395
The hematopoietic regulator TAL1 is required for chromatin looping between the β-globin LCR and human γ-globin genes to activate transcription
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4283–4293, https://doi.org/10.1093/nar/gku072
A bacteriophage transcription regulator inhibits bacterial transcription initiation by σ-factor displacement
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4294–4305, https://doi.org/10.1093/nar/gku080
Coordinated repressive chromatin-remodeling of Oct4 and Nanog genes in RA-induced differentiation of embryonic stem cells involves RIP140
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4306–4317, https://doi.org/10.1093/nar/gku092
DAXX co-folds with H3.3/H4 using high local stability conferred by the H3.3 variant recognition residues
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4318–4331, https://doi.org/10.1093/nar/gku090
The transcript elongation factor SPT4/SPT5 is involved in auxin-related gene expression in Arabidopsis
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4332–4347, https://doi.org/10.1093/nar/gku096
Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4348–4362, https://doi.org/10.1093/nar/gku100
Dissecting the function of the adult β-globin downstream promoter region using an artificial zinc finger DNA-binding domain
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4363–4374, https://doi.org/10.1093/nar/gku107
Direct activation of human and mouse Oct4 genes using engineered TALE and Cas9 transcription factors
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4375–4390, https://doi.org/10.1093/nar/gku109
Alternative Lengthening of Telomeres is characterized by reduced compaction of telomeric chromatin
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4391–4405, https://doi.org/10.1093/nar/gku114
Genome Integrity, Repair and Replication
Persistently stalled replication forks inhibit nucleotide excision repair in trans by sequestering Replication protein A
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4406–4413, https://doi.org/10.1093/nar/gkt1412
The α isoform of topoisomerase II is required for hypercompaction of mitotic chromosomes in human cells
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4414–4426, https://doi.org/10.1093/nar/gku076
Modulation of ATR-mediated DNA damage checkpoint response by cryptochrome 1
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4427–4434, https://doi.org/10.1093/nar/gku094
PARP1–TDP1 coupling for the repair of topoisomerase I–induced DNA damage
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4435–4449, https://doi.org/10.1093/nar/gku088
A dual promoter system regulating λ DNA replication initiation
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4450–4462, https://doi.org/10.1093/nar/gku103
DNA-PKcs is required to maintain stability of Chk1 and Claspin for optimal replication stress response
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4463–4473, https://doi.org/10.1093/nar/gku116
Genomics
Mapping of six somatic linker histone H1 variants in human breast cancer cells uncovers specific features of H1.2
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4474–4493, https://doi.org/10.1093/nar/gku079
Molecular Biology
Distinct functions of the RNA polymerase σ subunit region 3.2 in RNA priming and promoter escape
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4494–4504, https://doi.org/10.1093/nar/gkt1384
Folding a stable RNA pseudoknot through rearrangement of two hairpin structures
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4505–4515, https://doi.org/10.1093/nar/gkt1396
Functional signature for the recognition of specific target mRNAs by human Staufen1 protein
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4516–4526, https://doi.org/10.1093/nar/gku073
The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4527–4545, https://doi.org/10.1093/nar/gku075
An antisense promoter in mouse L1 retrotransposon open reading frame-1 initiates expression of diverse fusion transcripts and limits retrotransposition
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4546–4562, https://doi.org/10.1093/nar/gku091
BswR controls bacterial motility and biofilm formation in Pseudomonas aeruginosa through modulation of the small RNA rsmZ
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4563–4576, https://doi.org/10.1093/nar/gku106
Nucleic Acid Enzymes
Adjacent single-stranded regions mediate processing of tRNA precursors by RNase E direct entry
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4577–4589, https://doi.org/10.1093/nar/gkt1403
A widespread bacteriophage abortive infection system functions through a Type IV toxin–antitoxin mechanism
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4590–4605, https://doi.org/10.1093/nar/gkt1419
The omega subunit of the RNA polymerase core directs transcription efficiency in cyanobacteria
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4606–4614, https://doi.org/10.1093/nar/gku084
RNA
Stepwise assembly of multiple Lin28 proteins on the terminal loop of let-7 miRNA precursors
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4615–4628, https://doi.org/10.1093/nar/gkt1391
Differential RISC association of endogenous human microRNAs predicts their inhibitory potential
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4629–4639, https://doi.org/10.1093/nar/gkt1393
Interplay between pre-mRNA splicing and microRNA biogenesis within the supraspliceosome
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4640–4651, https://doi.org/10.1093/nar/gkt1413
Trypanosome MKT1 and the RNA-binding protein ZC3H11: interactions and potential roles in post-transcriptional regulatory networks
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4652–4668, https://doi.org/10.1093/nar/gkt1416
Antibiotic stress-induced modulation of the endoribonucleolytic activity of RNase III and RNase G confers resistance to aminoglycoside antibiotics in Escherichia coli
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4669–4681, https://doi.org/10.1093/nar/gku093
Curli synthesis and biofilm formation in enteric bacteria are controlled by a dynamic small RNA module made up of a pseudoknot assisted by an RNA chaperone
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4682–4696, https://doi.org/10.1093/nar/gku098
Structure-function analysis of the Yhc1 subunit of yeast U1 snRNP and genetic interactions of Yhc1 with Mud2, Nam8, Mud1, Tgs1, U1 snRNA, SmD3 and Prp28
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4697–4711, https://doi.org/10.1093/nar/gku097
Structural Biology
The crystal structure of TDP-43 RRM1-DNA complex reveals the specific recognition for UG- and TG-rich nucleic acids
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4712–4722, https://doi.org/10.1093/nar/gkt1407
Structural basis of sodium–potassium exchange of a human telomeric DNA quadruplex without topological conversion
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4723–4733, https://doi.org/10.1093/nar/gku083
Structure of a rare non-standard sequence k-turn bound by L7Ae protein
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4734–4740, https://doi.org/10.1093/nar/gku087
Structure of human RNA N6-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4741–4754, https://doi.org/10.1093/nar/gku085
Synthetic Biology and Chemistry
Expanding the zinc-finger recombinase repertoire: directed evolution and mutational analysis of serine recombinase specificity determinants
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4755–4766, https://doi.org/10.1093/nar/gkt1389
A ribozyme that triphosphorylates RNA 5′-hydroxyl groups
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4767–4778, https://doi.org/10.1093/nar/gkt1405
Rational optimization of tolC as a powerful dual selectable marker for genome engineering
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Pages 4779–4790, https://doi.org/10.1093/nar/gkt1374
Methods Online
Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Page e50, https://doi.org/10.1093/nar/gkt1406
Correction of sequence-dependent ambiguous bases (Ns) from the 454 pyrosequencing system
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Page e51, https://doi.org/10.1093/nar/gku070
Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Page e52, https://doi.org/10.1093/nar/gkt1411
S/MAR sequence confers long-term mitotic stability on non-integrating lentiviral vector episomes without selection
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Page e53, https://doi.org/10.1093/nar/gku082
A phylogenomics approach for selecting robust sets of phylogenetic markers
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Page e54, https://doi.org/10.1093/nar/gku071
A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Page e55, https://doi.org/10.1093/nar/gku077
Multiplexing clonality: combining RGB marking and genetic barcoding
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Page e56, https://doi.org/10.1093/nar/gku081
Hunting complex differential gene interaction patterns across molecular contexts
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Page e57, https://doi.org/10.1093/nar/gku086
Design and application of cotranscriptional non-enzymatic RNA circuits and signal transducers
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Page e58, https://doi.org/10.1093/nar/gku074
Improved search heuristics find 20 000 new alignments between human and mouse genomes
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Page e59, https://doi.org/10.1093/nar/gku104
EDDY: a novel statistical gene set test method to detect differential genetic dependencies
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Page e60, https://doi.org/10.1093/nar/gku099
Aptamer-guided gene targeting in yeast and human cells
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Page e61, https://doi.org/10.1093/nar/gku101
Front-Matter/Back-Matter
Nucleic Acids Research: VOLUME 42 ISSUE 7 2014
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Page i, https://doi.org/10.1093/nar/gku019
Nucleic Acids Research - Editorial Board
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Page ii, https://doi.org/10.1093/nar/gku042
Subscriptions
Nucleic Acids Research, Volume 42, Issue 7, 1 April 2014, Page iii, https://doi.org/10.1093/nar/gku065
