Volume 47, Issue 11
20 June 2019
Cover image
Cover image
Cover: Let’s go fishing! What a better way to assess the existence and prevalence of RNA G-quadruplexes (G4-RNAs) in vivo than fishing them out from human cells? To this end, biotinylated biomimetic quadruplex ligand BioTASQ were used as molecular baits to isolate G4s from human cells (MCF-7) through affinity pull-down strategies and identified them via the G4RP-RT-qPCR protocol (G4-RNA–specific precipitation & reverse transcription quantitative polymerase chain reaction). Collected results highlight the prevalence of G4-RNA in the human transcriptome, in both coding (VEGFA and NRAS) and non-coding RNAs (MALAT1, XIST and RPPH1).
For more information see the article by Renard, I. et al., pages 5502–5510, in this issue.
For more information see the article by Renard, I. et al., pages 5502–5510, in this issue.
ISSN 0305-1048
EISSN 1362-4962
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Volume 47, Issue 11, 20 June 2019
NAR Breakthrough Article
Site-specific replacement of phosphorothioate with alkyl phosphonate linkages enhances the therapeutic profile of gapmer ASOs by modulating interactions with cellular proteins
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5465–5479, https://doi.org/10.1093/nar/gkz247
Survey and Summary
The mitochondrial R-loop
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5480–5489, https://doi.org/10.1093/nar/gkz277
Beyond CLIP: advances and opportunities to measure RBP–RNA and RNA–RNA interactions
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5490–5501, https://doi.org/10.1093/nar/gkz295
Chemical Biology and Nucleic Acid Chemistry
Small-molecule affinity capture of DNA/RNA quadruplexes and their identification in vitro and in vivo through the G4RP protocol
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5502–5510, https://doi.org/10.1093/nar/gkz215
Carboxylate-functionalized foldamer inhibitors of HIV-1 integrase and Topoisomerase 1: artificial analogues of DNA mimic proteins
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5511–5521, https://doi.org/10.1093/nar/gkz352
DNA repair enzymes ALKBH2, ALKBH3, and AlkB oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in vitro
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5522–5529, https://doi.org/10.1093/nar/gkz395
Computational Biology
Quantifying the two-state facilitated diffusion model of protein–DNA interactions
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5530–5538, https://doi.org/10.1093/nar/gkz308
Fast hierarchical Bayesian analysis of population structure
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5539–5549, https://doi.org/10.1093/nar/gkz361
A multiscale analysis of DNA phase separation: from atomistic to mesoscale level
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5550–5562, https://doi.org/10.1093/nar/gkz377
Limits in accuracy and a strategy of RNA structure prediction using experimental information
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5563–5572, https://doi.org/10.1093/nar/gkz427
Gene Regulation, Chromatin and Epigenetics
PTEN interacts with the transcription machinery on chromatin and regulates RNA polymerase II-mediated transcription
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5573–5586, https://doi.org/10.1093/nar/gkz272
ONECUT transcription factors induce neuronal characteristics and remodel chromatin accessibility
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5587–5602, https://doi.org/10.1093/nar/gkz273
Interplay between small RNA pathways shapes chromatin landscapes in C. elegans
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5603–5616, https://doi.org/10.1093/nar/gkz275
DNA sequence influences hexasome orientation to regulate DNA accessibility
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5617–5633, https://doi.org/10.1093/nar/gkz283
A novel CRISPR-engineered prostate cancer cell line defines the AR-V transcriptome and identifies PARP inhibitor sensitivities
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5634–5647, https://doi.org/10.1093/nar/gkz286
Bacterial genome architecture shapes global transcriptional regulation by DNA supercoiling
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5648–5657, https://doi.org/10.1093/nar/gkz300
Reversible ADP-ribosylation of RNA
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5658–5669, https://doi.org/10.1093/nar/gkz305
Genome Integrity, Repair and Replication
SCRE serves as a unique synaptonemal complex fastener and is essential for progression of meiosis prophase I in mice
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5670–5683, https://doi.org/10.1093/nar/gkz226
KEOPS complex promotes homologous recombination via DNA resection
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5684–5697, https://doi.org/10.1093/nar/gkz228
A new role for Escherichia coli Dam DNA methylase in prevention of aberrant chromosomal replication
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5698–5711, https://doi.org/10.1093/nar/gkz242
Structural evidence for an essential Fe–S cluster in the catalytic core domain of DNA polymerase ϵ
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5712–5722, https://doi.org/10.1093/nar/gkz248
Replicative DNA polymerases promote active displacement of SSB proteins during lagging strand synthesis
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5723–5734, https://doi.org/10.1093/nar/gkz249
Genomics
HOT or not: examining the basis of high-occupancy target regions
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5735–5745, https://doi.org/10.1093/nar/gkz460
Molecular Biology
The mitoribosome-specific protein mS38 is preferentially required for synthesis of cytochrome c oxidase subunits
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5746–5760, https://doi.org/10.1093/nar/gkz266
Two classes of EF1-family translational GTPases encoded by giant viruses
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5761–5776, https://doi.org/10.1093/nar/gkz296
Non-canonical translation initiation in yeast generates a cryptic pool of mitochondrial proteins
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5777–5791, https://doi.org/10.1093/nar/gkz301
HCF-2 inhibits cell proliferation and activates differentiation-gene expression programs
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5792–5808, https://doi.org/10.1093/nar/gkz307
Nucleic Acid Enzymes
DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5809–5821, https://doi.org/10.1093/nar/gkz306
Programmable DNA cleavage by Ago nucleases from mesophilic bacteria Clostridium butyricum and Limnothrix rosea
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5822–5836, https://doi.org/10.1093/nar/gkz379
Ebola virus VP35 has novel NTPase and helicase-like activities
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5837–5851, https://doi.org/10.1093/nar/gkz340
Myg1 exonuclease couples the nuclear and mitochondrial translational programs through RNA processing
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5852–5866, https://doi.org/10.1093/nar/gkz371
RNA and RNA-protein complexes
Increased versatility despite reduced molecular complexity: evolution, structure and function of metazoan splicing factor PRPF39
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5867–5879, https://doi.org/10.1093/nar/gkz243
Primed adaptation tolerates extensive structural and size variations of the CRISPR RNA guide in Haloarcula hispanica
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5880–5891, https://doi.org/10.1093/nar/gkz244
Proteomic and transcriptomic experiments reveal an essential role of RNA degradosome complexes in shaping the transcriptome of Mycobacterium tuberculosis
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5892–5905, https://doi.org/10.1093/nar/gkz251
Maturation of atypical ribosomal RNA precursors in Helicobacter pylori
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5906–5921, https://doi.org/10.1093/nar/gkz258
Interplay of primary sequence, position and secondary RNA structure determines alternative splicing of LMNA in a pre-mature aging syndrome
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5922–5935, https://doi.org/10.1093/nar/gkz259
Impact of intron removal from tRNA genes on Saccharomyces cerevisiae
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5936–5949, https://doi.org/10.1093/nar/gkz270
Structural Biology
Structures of maintenance of carboxysome distribution Walker-box McdA and McdB adaptor homologs
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5950–5962, https://doi.org/10.1093/nar/gkz314
Structure-guided post-SELEX optimization of an ochratoxin A aptamer
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5963–5972, https://doi.org/10.1093/nar/gkz336
Crystal structure of the Trypanosoma cruzi EIF4E5 translation factor homologue in complex with mRNA cap-4
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5973–5987, https://doi.org/10.1093/nar/gkz339
Alternative σI/anti-σI factors represent a unique form of bacterial σ/anti-σ complex
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5988–5997, https://doi.org/10.1093/nar/gkz355
Synthetic Biology and Bioengineering
Targeted amplification of a sequence of interest in artificial chromosome in mammalian cells
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 5998–6006, https://doi.org/10.1093/nar/gkz343
Self-powered RNA nanomachine driven by metastable structure
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Pages 6007–6014, https://doi.org/10.1093/nar/gkz364
Methods Online
A panel of colorimetric assays to measure enzymatic activity in the base excision DNA repair pathway
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Page e61, https://doi.org/10.1093/nar/gkz171
Cell-specific network constructed by single-cell RNA sequencing data
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Page e62, https://doi.org/10.1093/nar/gkz172
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Page e63, https://doi.org/10.1093/nar/gkz173
AlleleHMM: a data-driven method to identify allele specific differences in distributed functional genomic marks
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Page e64, https://doi.org/10.1093/nar/gkz176
MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Page e65, https://doi.org/10.1093/nar/gkz201
Cell lineage and communication network inference via optimization for single-cell transcriptomics
Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Page e66, https://doi.org/10.1093/nar/gkz204
