Subject: Nucleic Acids Research Table of Contents for 6 April 2018 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Nucleic Acids Research  
Volume 46 Issue 6
 
6 April 2018
 
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SURVEY AND SUMMARY
 
 
 
Capturing the ome': the expanding molecular toolbox for RNA and DNA library construction border= 
 
Morgane Boone; Andries De Koker; Nico Callewaert
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Characterization of clinically used oral antiseptics as quadruplex-binding ligands 
 
David R Calabrese; Katherine Zlotkowski; Stephanie Alden; William M Hewitt; Colleen M Connelly ...
 
 
Di-copper metallodrugs promote NCI-60 chemotherapy via singlet oxygen and superoxide production with tandem TA/TA and AT/AT oligonucleotide discrimination border= 
 
Creina Slator; Zara Molphy; Vickie McKee; Conor Long ; Tom Brown ...
 
 
i-Clamp phenoxazine for the fine tuning of DNA i-motif stability border= 
 
Vladimir B Tsvetkov; Timofei S Zatsepin; Evgeny S Belyaev; Yury I Kostyukevich; George V Shpakovski ...
 
 
Enzymatic synthesis of cyclic dinucleotide analogs by a promiscuous cyclic-AMP-GMP synthetase and analysis of cyclic dinucleotide responsive riboswitches border= 
 
Katherine D Launer-Felty; Scott A Strobel
 
 
 
 
Computational Biology
 
 
 
Metaviz: interactive statistical and visual analysis of metagenomic data border= 
 
Justin Wagner; Florin Chelaru; Jayaram Kancherla; Joseph N Paulson ; Alexander Zhang ...
 
 
DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations border= 
 
Giovanni B Brandani; Toru Niina; Cheng Tan; Shoji Takada
 
 
Data Resources and Analyses
 
 
 
Translational profiling of B cells infected with the Epstein-Barr virus reveals 5 leader ribosome recruitment through upstream open reading frames border= 
 
Maja Bencun ; Olaf Klinke; Agnes Hotz-Wagenblatt; Severina Klaus; Ming-Han Tsai ...
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
TelAP1 links telomere complexes with developmental expression site silencing in African trypanosomes border= 
 
Helena Reis; Marie Schwebs ; Sabrina Dietz; Christian J Janzen; Falk Butter
 
 
Cell-cycle regulation of non-enzymatic functions of the Drosophila methyltransferase PR-Set7 border= 
 
Amel Zouaz; Céline Fernando; Yannick Perez ; Claude Sardet; Eric Julien ...
 
 
 
 
A context-specific cardiac beta -catenin and GATA4 interaction influences TCF7L2 occupancy and remodels chromatin driving disease progression in the adult heart border= 
 
Lavanya M Iyer; Sankari Nagarajan; Monique Woelfer; Eric Schoger ; Sara Khadjeh ...
 
 
Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer'promoter contacts border= 
 
Verena Thormann; Maika C Rothkegel; Robert Schöpflin; Laura V Glaser; Petar Djuric ...
 
 
Decoding the dynamic DNA methylation and hydroxymethylation landscapes in endodermal lineage intermediates during pancreatic differentiation of hESC border= 
 
Jia Li; Xinwei Wu; Yubin Zhou; Minjung Lee; Lei Guo ...
 
 
Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP border= 
 
Donghyuk Kim ; Sang Woo Seo; Ye Gao; Hojung Nam; Gabriela I Guzman ...
 
 
Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations border= 
 
Nela Nikolic; Tobias Bergmiller ; Alexandra Vandervelde; Tanino G Albanese; Lendert Gelens ...
 
 
Genome Integrity, Repair and Replication
 
 
 
Replication stress induces accumulation of FANCD2 at central region of large fragile genes border= 
 
Yusuke Okamoto; Watal M Iwasaki ; Kazuto Kugou; Kazuki K Takahashi; Arisa Oda ...
 
 
DNA mismatch repair and oligonucleotide end-protection promote base-pair substitution distal from a CRISPR/Cas9-induced DNA break border=  
 
Tim Harmsen; Sjoerd Klaasen; Henri van de Vrugt ; Hein te Riele
 
 
Missed cleavage opportunities by FEN1 lead to Okazaki fragment maturation via the long-flap pathway border= 
 
Manal S Zaher; Fahad Rashid; Bo Song; Luay I Joudeh; Mohamed A Sobhy ...
 
 
Nuclear import of Cdc13 limits chromosomal capping border= 
 
Sofiane Y Mersaoui ; Erin Bonnell; Raymund J Wellinger
 
 
Structurally distinct Mre11 domains mediate MRX functions in resection, end-tethering and DNA damage resistance border= 
 
Corinne Cassani; Elisa Gobbini; Jacopo Vertemara; Weibin Wang ; Antonio Marsella ...
 
 
Genomics
 
 
 
The association between copy number aberration, DNA methylation and gene expression in tumor samples border= 
 
Wei Sun; Paul Bunn; Chong Jin; Paul Little; Vasyl Zhabotynsky ...
 
 
Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana border= 
 
Lauriane Simon ; Fernando A Rabanal; Tristan Dubos; Cecilia Oliver; Damien Lauber ...
 
 
Molecular Biology
 
 
 
Structural rearrangements in the mitochondrial genome of Drosophila melanogaster induced by elevated levels of the replicative DNA helicase border= 
 
Grzegorz L Ciesielski; Cristina A Nadalutti ; Marcos T Oliveira; Howard T Jacobs; Jack D Griffith ...
 
 
Ksp1-dependent phosphorylation of eIF4G modulates post-transcriptional regulation of specific mRNAs under glucose deprivation conditions border=  
 
Yeonji Chang; Won-Ki Huh
 
 
Arginine methylation of the C-terminus RGG motif promotes TOP3B topoisomerase activity and stress granule localization border= 
 
Lifeng Huang ; Zhihao Wang; Nithya Narayanan; Yanzhong Yang
 
 
eIF4A alleviates the translational repression mediated by classical secondary structures more than by G-quadruplexes border= 
 
Joseph A Waldron; Farheen Raza; John Le Quesne
 
 
Nucleic Acid Enzymes
 
 
 
Direct observation of nucleic acid binding dynamics by the telomerase essential N-terminal domain border= 
 
Shankar Shastry; Olga Steinberg-Neifach; Neal Lue; Michael D Stone
 
 
Investigation of sliding DNA clamp dynamics by single-molecule fluorescence, mass spectrometry and structure-based modeling border= 
 
Varun V Gadkari; Sophie R Harvey; Austin T Raper; Wen-Ting Chu ; Jin Wang ...
 
 
Noncanonical substrate preference of lambda exonuclease for 5-nonphosphate-ended dsDNA and a mismatch-induced acceleration effect on the enzymatic reaction border= 
 
Tongbo Wu; Yufei Yang; Wei Chen; Jiayu Wang ; Ziyu Yang ...
 
 
The DNMT3A R882H mutant displays altered flanking sequence preferences border= 
 
Max Emperle; Arumugam Rajavelu; Stefan Kunert; Paola B Arimondo; Richard Reinhardt ...
 
 
RNA and RNA-protein complexes
 
 
 
Viewing pre-60S maturation at a minute's timescale border= 
 
Gertrude Zisser ; Uli Ohmayer; Christina Mauerhofer; Valentin Mitterer; Isabella Klein ...
 
 
An engineered RNA binding protein with improved splicing regulation border= 
 
Melissa A Hale; Jared I Richardson ; Ryan C Day; Ona L McConnell; Juan Arboleda ...
 
 
Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis border= 
 
Neelam Shah; Simone A Beckham; Jacqueline A Wilce ; Matthew C J Wilce
 
 
Viral suppressors of RNAi employ a rapid screening mode to discriminate viral RNA from cellular small RNA border= 
 
Mohamed Fareh; Jasper van Lopik; Iason Katechis; Alfred W Bronkhorst; Anna C Haagsma ...
 
 
Cold-inducible RNA-binding protein (CIRP) induces translation of the cell-cycle inhibitor p27Kip1 border= 
 
Martina Roilo ; Michael K Kullmann; Ludger Hengst
 
 
Structural Biology
 
 
 
The structure of an elongation factor G-ribosome complex captured in the absence of inhibitors border= 
 
Kevin Macé; Emmanuel Giudice; Sophie Chat; Reynald Gillet
 
 
Structural and mechanistic insights into UHRF1-mediated DNMT1 activation in the maintenance DNA methylation border= 
 
Tao Li ; Linsheng Wang; Yongming Du; Si Xie; Xi Yang ...
 
 
The C-terminal helix of ribosomal P stalk recognizes a hydrophobic groove of elongation factor 2 in a novel fashion border= 
 
Takehito Tanzawa ; Koji Kato; Dylan Girodat; Toyoyuki Ose; Yuki Kumakura ...
 
 
Structural insights into the unique mechanism of transcription activation by Caulobacter crescentus GcrA border= 
 
Xiaoxian Wu; Diane L Haakonsen ; Allen G Sanderlin; Yue J Liu; Liqiang Shen ...
 
 
Erratum
 
 
 
Viral suppressors of RNAi employ a rapid screening mode to discriminate viral RNA from cellular small RNA border= 
 
Mohamed Fareh; Jasper van Lopik; Iason Katechis; Alfred W Bronkhorst; Anna C Haagsma ...
 
 
Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer'promoter contacts border=  
 
Verena Thormann; Maika C Rothkegel; Robert Schöpflin ; Laura V Glaser; Petar Djuric ...
 
 
Methods Online
 
 
 
TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information border= 
 
Shubhada R Kulkarni; Dries Vaneechoutte; Jan Van de Velde; Klaas Vandepoele
 
 
XPAT: a toolkit to conduct cross-platform association studies with heterogeneous sequencing datasets border= 
 
Yao Yu ; Hao Hu; Ryan J Bohlender; Fulan Hu; Jiun-Sheng Chen ...
 
 
HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks  
 
Ariful Azad; Georgios A Pavlopoulos; Christos A Ouzounis ; Nikos C Kyrpides; Aydin Buluç
 
 
Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infection border= 
 
Heeju Noh; Jason E Shoemaker; Rudiyanto Gunawan
 
 
PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures border= 
 
Pawel S Krawczyk; Leszek Lipinski ; Andrzej Dziembowski
 
 
dropClust: efficient clustering of ultra-large scRNA-seq data border= 
 
Debajyoti Sinha; Akhilesh Kumar; Himanshu Kumar; Sanghamitra Bandyopadhyay; Debarka Sengupta
 
 
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