Volume 46, Issue 16
19 September 2018
ISSN 0305-1048
EISSN 1362-4962
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Volume 46, Issue 16, 19 September 2018
Survey and Summary
Insights into the development of chemical probes for RNA
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8025–8037, https://doi.org/10.1093/nar/gky718
Tags:
ligands, rna, small molecule
i-Motif DNA: structural features and significance to cell biology
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8038–8056, https://doi.org/10.1093/nar/gky735
Tags:
base pairing, dna, stabilization, cellular biology
Chemical Biology and Nucleic Acid Chemistry
In vitro selection of an XNA aptamer capable of small-molecule recognition
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8057–8068, https://doi.org/10.1093/nar/gky667
A strongly pairing fifth base: oligonucleotides with a C-nucleoside replacing thymidine
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8069–8078, https://doi.org/10.1093/nar/gky669
Tags:
base pairing, dna, nucleosides, oligonucleotides, pyridines
Small synthetic molecule-stabilized RNA pseudoknot as an activator for –1 ribosomal frameshifting
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8079–8089, https://doi.org/10.1093/nar/gky689
Structural basis for the synergy of 4′- and 2′-modifications on siRNA nuclease resistance, thermal stability and RNAi activity
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8090–8104, https://doi.org/10.1093/nar/gky703
Computational Biology
A deep recurrent neural network discovers complex biological rules to decipher RNA protein-coding potential
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8105–8113, https://doi.org/10.1093/nar/gky567
Tags:
codon nucleotides, rna, rna, messenger, deep learning, genome
A genome-wide scan for correlated mutations detects macromolecular and chromatin interactions in Arabidopsis thaliana
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8114–8132, https://doi.org/10.1093/nar/gky576
AptaBlocks: Designing RNA complexes and accelerating RNA-based drug delivery systems
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8133–8142, https://doi.org/10.1093/nar/gky577
Tags:
complex, drug delivery systems, molecule, rna, pancreatic cancer
Characterizing the 3D structure and dynamics of chromosomes and proteins in a common contact matrix framework
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8143–8152, https://doi.org/10.1093/nar/gky604
Data Resources and Analyses
Revealing a human p53 universe
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8153–8167, https://doi.org/10.1093/nar/gky720
Tags:
datasets, gene expression, genes, genome, consensus
Circular RNA expression in human hematopoietic cells is widespread and cell-type specific
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8168–8180, https://doi.org/10.1093/nar/gky721
Gene Regulation, Chromatin and Epigenetics
The sequence features that define efficient and specific hAGO2-dependent miRNA silencing guides
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8181–8196, https://doi.org/10.1093/nar/gky546
Tags:
base pairing, micrornas, mismatch, rna, rna, messenger
Histone variant H2A.Z deposition and acetylation directs the canonical Notch signaling response
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8197–8215, https://doi.org/10.1093/nar/gky551
Faithful chromosome segregation in Trypanosoma brucei requires a cohort of divergent spindle-associated proteins with distinct functions
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8216–8231, https://doi.org/10.1093/nar/gky557
RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8232–8244, https://doi.org/10.1093/nar/gky562
A multivariate prediction model for Rho-dependent termination of transcription
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8245–8260, https://doi.org/10.1093/nar/gky563
Tags:
dna, genome, rna, templates, open reading frames
Rpd3L HDAC links H3K4me3 to transcriptional repression memory
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8261–8274, https://doi.org/10.1093/nar/gky573
Genome Integrity, Repair and Replication
Efficient CRISPR/Cas9-mediated editing of trinucleotide repeat expansion in myotonic dystrophy patient-derived iPS and myogenic cells
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8275–8298, https://doi.org/10.1093/nar/gky548
Tags:
crispr, rna, guide, excision, gene editing, myotonic dystrophy
Germline DNA replication timing shapes mammalian genome composition
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8299–8310, https://doi.org/10.1093/nar/gky610
Tags:
dna replication, genes, genome, germ cells, mammals
ATR-mediated proteome remodeling is a major determinant of homologous recombination capacity in cancer cells
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8311–8325, https://doi.org/10.1093/nar/gky625
Combined deficiency of Senataxin and DNA-PKcs causes DNA damage accumulation and neurodegeneration in spinal muscular atrophy
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8326–8346, https://doi.org/10.1093/nar/gky641
Tags:
dna, dna damage, mice, nerve degeneration, neurons
The helicase Pif1 functions in the template switching pathway of DNA damage bypass
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8347–8356, https://doi.org/10.1093/nar/gky648
The signature motif of the Saccharomyces cerevisiae Pif1 DNA helicase is essential in vivo for mitochondrial and nuclear functions and in vitro for ATPase activity
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8357–8370, https://doi.org/10.1093/nar/gky655
Genomics
Shared nucleotide flanks confer transcriptional competency to bZip core motifs
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8371–8384, https://doi.org/10.1093/nar/gky681
In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8385–8403, https://doi.org/10.1093/nar/gky692
Tags:
androstanes, genes, genome, liver, mice
Molecular Biology
mRNAs are sorted for export or degradation before passing through nuclear speckles
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8404–8416, https://doi.org/10.1093/nar/gky650
Tags:
catabolism, exosomes, rna, rna, messenger
Decoding non-random mutational signatures at Cas9 targeted sites
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8417–8434, https://doi.org/10.1093/nar/gky653
Tags:
dna, genetics, genome, genome editing, mammals
MTG1 couples mitoribosome large subunit assembly with intersubunit bridge formation
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8435–8453, https://doi.org/10.1093/nar/gky672
HIV-1 Vpr and p21 restrict LINE-1 mobility
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8454–8470, https://doi.org/10.1093/nar/gky688
The human Obg protein GTPBP10 is involved in mitoribosomal biogenesis
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8471–8482, https://doi.org/10.1093/nar/gky701
Nucleic Acid Enzymes
Evolutionary insights into Trm112-methyltransferase holoenzymes involved in translation between archaea and eukaryotes
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8483–8499, https://doi.org/10.1093/nar/gky638
Tags:
archaea, complex, enzymes, eukaryotic cells, holoenzymes
Single molecule kinetics uncover roles for E. coli RecQ DNA helicase domains and interaction with SSB
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8500–8515, https://doi.org/10.1093/nar/gky647
Tags:
dna, dna helicases, kinetics, molecule, translocation (genetics)
The Pif1 signature motif of Pfh1 is necessary for both protein displacement and helicase unwinding activities, but is dispensable for strand-annealing activity
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8516–8531, https://doi.org/10.1093/nar/gky654
Tags:
dna, rna, mutation, oligonucleotides, mechlorethamine
Entropy-driven DNA logic circuits regulated by DNAzyme
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8532–8541, https://doi.org/10.1093/nar/gky663
Tags:
catalysis, dna, dna, catalytic, entropy, logic
RNA and RNA-protein complexes
Structural accommodations accompanying splicing of a group II intron RNP
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8542–8556, https://doi.org/10.1093/nar/gky416
Tags:
dna, introns, rna, rna splicing, exons
SWI/SNF interacts with cleavage and polyadenylation factors and facilitates pre-mRNA 3′ end processing
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8557–8573, https://doi.org/10.1093/nar/gky438
Computational analysis of ribonomics datasets identifies long non-coding RNA targets of γ-herpesviral miRNAs
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8574–8589, https://doi.org/10.1093/nar/gky459
Structural insights into Drosophila-C3PO complex assembly and ‘Dynamic Side Port’ model in substrate entry and release
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8590–8604, https://doi.org/10.1093/nar/gky465
Tags:
drosophila, rna, crystal structure
The essential nature of YqfG, a YbeY homologue required for 3′ maturation of Bacillus subtilis 16S ribosomal RNA is suppressed by deletion of RNase R
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8605–8615, https://doi.org/10.1093/nar/gky488
Structural Biology
DNA binding with a minimal scaffold: structure–function analysis of Lig E DNA ligases
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8616–8629, https://doi.org/10.1093/nar/gky622
Tags:
dna, dna ligases
Crystal structure of dimeric human PNPase reveals why disease-linked mutants suffer from low RNA import and degradation activities
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8630–8640, https://doi.org/10.1093/nar/gky642
Tags:
catabolism, crystal structure, rna, mitochondria, mutation
E. coli elongation factor Tu bound to a GTP analogue displays an open conformation equivalent to the GDP-bound form
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8641–8650, https://doi.org/10.1093/nar/gky697
Structural dynamics of translation elongation factor Tu during aa-tRNA delivery to the ribosome
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8651–8661, https://doi.org/10.1093/nar/gky651
Corrigendum
RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8662, https://doi.org/10.1093/nar/gky617
EVI1 carboxy-terminal phosphorylation is ATM-mediated and sustains transcriptional modulation and self-renewal via enhanced CtBP1 association
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8663, https://doi.org/10.1093/nar/gky711
Generating genomic platforms to study Candida albicans pathogenesis
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages 8664, https://doi.org/10.1093/nar/gky747
Methods Online
SB Driver Analysis: a Sleeping Beauty cancer driver analysis framework for identifying and prioritizing experimentally actionable oncogenes and tumor suppressors
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages e94, https://doi.org/10.1093/nar/gky450
Triazole linking for preparation of a next-generation sequencing library from single-stranded DNA
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages e95, https://doi.org/10.1093/nar/gky452
BASiNET—BiologicAl Sequences NETwork: a case study on coding and non-coding RNAs identification
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages e96, https://doi.org/10.1093/nar/gky462
RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages e97, https://doi.org/10.1093/nar/gky486
Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages e98, https://doi.org/10.1093/nar/gky496
Tags:
cytokinesis, hiv-1, rna
A novel λ integrase-mediated seamless vector transgenesis platform for therapeutic protein expression
Nucleic Acids Research, Volume 46, Issue 16, 19 September 2018, Pages e99, https://doi.org/10.1093/nar/gky500
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Cover Image
Cover Image
Cover: Efficient excision of expanded pathogenic CTG repeats using CRISPR/Cas in myotonic dystrophy type 1 (DM1) patient-derived induced pluripotent stem cells (iPSCs). The illustration is based on fluorescent in situ hybridisation (FISH) that features CRISPR/Cas-corrected DM1-iPSCs with no ribonuclear foci (bottom right) compared to non-corrected DM1-iPSCs containing multiple punctated ribonuclear foci (top left). The ribonuclear foci are stained red (Cy3) while the nuclear DNA is stained blue (DAPI).
For more information, see article by Dastidar, S. et al., pages 8275–8298 in this issue. - Front Matter
- Table of Contents
- Back Matter
