Volume 45, Issue 10
2 June 2017
Cover image
Cover image
Cover: Ionizing radiation can cause DNA double strand breaks that often contain DNA end structures such as 5΄-hydroxyl or 3΄-phosphate groups incompatible with ligation and repair.
For more information see article by Aceytuno, R.D. et al., pages 6238–6251 in this issue.
For more information see article by Aceytuno, R.D. et al., pages 6238–6251 in this issue.
ISSN 0305-1048
EISSN 1362-4962
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Volume 45, Issue 10, 2 June 2017
Chemical Biology and Nucleic Acid Chemistry
Synthesis and polymerase activity of a fluorescent cytidine TNA triphosphate analogue
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5629–5638, https://doi.org/10.1093/nar/gkx368
Computational Biology
Global miRNA expression analysis identifies novel key regulators of plasma cell differentiation and malignant plasma cell
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5639–5652, https://doi.org/10.1093/nar/gkx327
Exploring genetic associations with ceRNA regulation in the human genome
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5653–5665, https://doi.org/10.1093/nar/gkx331
Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5666–5677, https://doi.org/10.1093/nar/gkx358
Data Resources and Analyses
ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5678–5690, https://doi.org/10.1093/nar/gkx270
Gene Regulation, Chromatin and Epigenetics
H3.Y discriminates between HIRA and DAXX chaperone complexes and reveals unexpected insights into human DAXX-H3.3-H4 binding and deposition requirements
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5691–5706, https://doi.org/10.1093/nar/gkx131
Structural and mechanistic insights into regulation of HBO1 histone acetyltransferase activity by BRPF2
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5707–5719, https://doi.org/10.1093/nar/gkx142
A class of circadian long non-coding RNAs mark enhancers modulating long-range circadian gene regulation
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5720–5738, https://doi.org/10.1093/nar/gkx156
ICF-specific DNMT3B dysfunction interferes with intragenic regulation of mRNA transcription and alternative splicing
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5739–5756, https://doi.org/10.1093/nar/gkx163
ChIP-seq analysis of the LuxR-type regulator VjbR reveals novel insights into the Brucella virulence gene expression network
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5757–5769, https://doi.org/10.1093/nar/gkx165
Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5770–5784, https://doi.org/10.1093/nar/gkx167
Trypanosoma brucei RAP1 maintains telomere and subtelomere integrity by suppressing TERRA and telomeric RNA:DNA hybrids
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5785–5796, https://doi.org/10.1093/nar/gkx184
New inhibitor targeting human transcription factor HSF1: effects on the heat shock response and tumor cell survival
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5797–5817, https://doi.org/10.1093/nar/gkx194
Genome urbanization: clusters of topologically co-regulated genes delineate functional compartments in the genome of Saccharomyces cerevisiae
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5818–5828, https://doi.org/10.1093/nar/gkx198
Functional anatomy of the immunoglobulin heavy chain 3΄ super-enhancer needs not only core enhancer elements but also their unique DNA context
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5829–5837, https://doi.org/10.1093/nar/gkx203
Genome Integrity, Repair and Replication
Telomere associated primase Tap repairs truncated telomeres of Streptomyces
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5838–5849, https://doi.org/10.1093/nar/gkx189
Yeast Sub1 and human PC4 are G-quadruplex binding proteins that suppress genome instability at co-transcriptionally formed G4 DNA
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5850–5862, https://doi.org/10.1093/nar/gkx201
Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens: characterization of a new class of UDG with broad substrate specificity
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5863–5876, https://doi.org/10.1093/nar/gkx209
A non-catalytic role of RecBCD in homology directed gap repair and translesion synthesis
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5877–5886, https://doi.org/10.1093/nar/gkx217
The SWI/SNF ATP-dependent nucleosome remodeler promotes resection initiation at a DNA double-strand break in yeast
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5887–5900, https://doi.org/10.1093/nar/gkx221
DICER and ZRF1 contribute to chromatin decondensation during nucleotide excision repair
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5901–5912, https://doi.org/10.1093/nar/gkx261
Molecular Biology
Guanine quadruplex monoclonal antibody 1H6 cross-reacts with restrained thymidine-rich single stranded DNA
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5913–5919, https://doi.org/10.1093/nar/gkx245
Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5920–5929, https://doi.org/10.1093/nar/gkx280
Identification of miRNA-7 by genome-wide analysis as a critical sensitizer for TRAIL-induced apoptosis in glioblastoma cells
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5930–5944, https://doi.org/10.1093/nar/gkx317
Proteomic analysis of polyribosomes identifies splicing factors as potential regulators of translation during mitosis
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5945–5957, https://doi.org/10.1093/nar/gkx326
Nucleic Acid Enzymes
A non-canonical multisubunit RNA polymerase encoded by the AR9 phage recognizes the template strand of its uracil-containing promoters
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5958–5967, https://doi.org/10.1093/nar/gkx264
The dynamics of the monomeric restriction endonuclease BcnI during its interaction with DNA
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5968–5979, https://doi.org/10.1093/nar/gkx294
Downstream element determines RNase Y cleavage of the saePQRS operon in Staphylococcus aureus
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5980–5994, https://doi.org/10.1093/nar/gkx296
Roles of the C-terminal domains of topoisomerase IIα and topoisomerase IIβ in regulation of the decatenation checkpoint
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 5995–6010, https://doi.org/10.1093/nar/gkx325
RNA
Coordination among tertiary base pairs results in an efficient frameshift-stimulating RNA pseudoknot
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6011–6022, https://doi.org/10.1093/nar/gkx134
N1-methyl-pseudouridine in mRNA enhances translation through eIF2α-dependent and independent mechanisms by increasing ribosome density
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6023–6036, https://doi.org/10.1093/nar/gkx135
Comparative analyses of the thermodynamic RNA binding signatures of different types of RNA recognition motifs
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6037–6050, https://doi.org/10.1093/nar/gkx136
N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6051–6063, https://doi.org/10.1093/nar/gkx141
AUF1 facilitates microRNA-mediated gene silencing
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6064–6073, https://doi.org/10.1093/nar/gkx149
sCLIP—an integrated platform to study RNA–protein interactomes in biomedical research: identification of CSTF2tau in alternative processing of small nuclear RNAs
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6074–6086, https://doi.org/10.1093/nar/gkx152
RNA–protein interactions govern antiviral specificity and encapsidation of broad spectrum anti-HIV reverse transcriptase aptamers
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6087–6097, https://doi.org/10.1093/nar/gkx155
Random pseuoduridylation in vivo reveals critical region of Escherichia coli 23S rRNA for ribosome assembly
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6098–6108, https://doi.org/10.1093/nar/gkx160
Melting temperature highlights functionally important RNA structure and sequence elements in yeast mRNA coding regions
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6109–6118, https://doi.org/10.1093/nar/gkx161
The pentatricopeptide repeat protein MTSF2 stabilizes a nad1 precursor transcript and defines the 3΄ end of its 5΄-half intron
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6119–6134, https://doi.org/10.1093/nar/gkx162
FASTKD1 and FASTKD4 have opposite effects on expression of specific mitochondrial RNAs, depending upon their endonuclease-like RAP domain
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6135–6146, https://doi.org/10.1093/nar/gkx164
The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6147–6167, https://doi.org/10.1093/nar/gkx168
A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6168–6176, https://doi.org/10.1093/nar/gkx170
TDP-43 suppresses tau expression via promoting its mRNA instability
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6177–6193, https://doi.org/10.1093/nar/gkx175
Genome-wide mapping of infection-induced SINE RNAs reveals a role in selective mRNA export
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6194–6208, https://doi.org/10.1093/nar/gkx180
Structural Biology
The crystal structure of Trz1, the long form RNase Z from yeast
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6209–6216, https://doi.org/10.1093/nar/gkx216
Structure of acid deoxyribonuclease
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6217–6227, https://doi.org/10.1093/nar/gkx222
Structural basis for the D-stereoselectivity of human DNA polymerase β
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6228–6237, https://doi.org/10.1093/nar/gkx252
Structural and functional characterization of the PNKP–XRCC4–LigIV DNA repair complex
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6238–6251, https://doi.org/10.1093/nar/gkx275
Expression of Concern
Detection of G-quadruplex DNA in mammalian cells
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page 6252, https://doi.org/10.1093/nar/gkx300
Guanine quadruplex structures localize to heterochromatin
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page 6253, https://doi.org/10.1093/nar/gkx301
Corrigendum
ADPriboDB: The database of ADP-ribosylated proteins
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page 6254, https://doi.org/10.1093/nar/gkx035
Structural basis for the Smad5 MH1 domain to recognize different DNA sequences
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Pages 6255–6257, https://doi.org/10.1093/nar/gkx226
Methods Online
MosaicHunter: accurate detection of postzygotic single-nucleotide mosaicism through next-generation sequencing of unpaired, trio, and paired samples
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e76, https://doi.org/10.1093/nar/gkx024
Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e77, https://doi.org/10.1093/nar/gkx026
Extensive libraries of gene truncation variants generated by in vitro transposition
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e78, https://doi.org/10.1093/nar/gkx030
Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e79, https://doi.org/10.1093/nar/gkx033
AssemblX: a user-friendly toolkit for rapid and reliable multi-gene assemblies
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e80, https://doi.org/10.1093/nar/gkx034
IC-Finder: inferring robustly the hierarchical organization of chromatin folding
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e81, https://doi.org/10.1093/nar/gkx036
Accurately annotate compound effects of genetic variants using a context-sensitive framework
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e82, https://doi.org/10.1093/nar/gkx041
BrainScope: interactive visual exploration of the spatial and temporal human brain transcriptome
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e83, https://doi.org/10.1093/nar/gkx046
DRNApred, fast sequence-based method that accurately predicts and discriminates DNA- and RNA-binding residues
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e84, https://doi.org/10.1093/nar/gkx059
Dynamic chromatin accessibility modeled by Markov process of randomly-moving molecules in the 3D genome
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e85, https://doi.org/10.1093/nar/gkx086
Discovery of cancer common and specific driver gene sets
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e86, https://doi.org/10.1093/nar/gkx089
Removing bias against short sequences enables northern blotting to better complement RNA-seq for the study of small RNAs
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e87, https://doi.org/10.1093/nar/gkx091
An accurate and efficient method for large-scale SSR genotyping and applications
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e88, https://doi.org/10.1093/nar/gkx093
Use of mariner transposases for one-step delivery and integration of DNA in prokaryotes and eukaryotes by transfection
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e89, https://doi.org/10.1093/nar/gkx113
A branch-migration based fluorescent probe for straightforward, sensitive and specific discrimination of DNA mutations
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e90, https://doi.org/10.1093/nar/gkx117
RCAS: an RNA centric annotation system for transcriptome-wide regions of interest
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e91, https://doi.org/10.1093/nar/gkx120
Stabilization of RNA hairpins using non-nucleotide linkers and circularization
Nucleic Acids Research, Volume 45, Issue 10, 2 June 2017, Page e92, https://doi.org/10.1093/nar/gkx122
