Subject: Nucleic Acids Research Table of Contents for 16 February 2018 Oxford Academic
 
 
 
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Nucleic Acids Research  
Volume 46 Issue 3
 
16 February 2018
 
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NAR Breakthrough Article
 
 
 
Prespacer processing and specific integration in a Type I-A CRISPR system border= 
 
Clare Rollie; Shirley Graham; Christophe Rouillon; Malcolm F White
 
 
SURVEY AND SUMMARY
 
 
 
Triplex-forming oligonucleotides: a third strand for DNA nanotechnology border= 
 
Arun Richard Chandrasekaran ; David A Rusling
 
 
Nonsense-mediated mRNA decay: a śnonsense' pathway makes sense in stem cell biology border= 
 
Xin Han; Yanling Wei; Hua Wang; Feilong Wang; Zhenyu Ju ...
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Triggering nucleic acid nanostructure assembly by conditional kissing interactions border= 
 
Laurent Azéma ; Servane Bonnet-Salomon; Masayuki Endo; Yosuke Takeuchi; Guillaume Durand ...
 
 
Selective alkylation of T'T mismatched DNA using vinyldiaminotriazine'acridine conjugate border= 
 
Kazumitsu Onizuka; Akira Usami ; Yudai Yamaoki; Tomohito Kobayashi; Madoka E Hazemi ...
 
 
 
 
Computational Biology
 
 
 
Transcriptional interference by small transcripts in proximal promoter regions border= 
 
Amit Pande; Jürgen Brosius; Izabela Makalowska ; Wojciech Makalowski; Carsten A Raabe
 
 
Integrative analysis reveals disrupted pathways regulated by microRNAs in cancer border= 
 
Gary Wilk; Rosemary Braun
 
 
A coarse-grained model for DNA origami border= 
 
Roman V Reshetnikov; Anastasia V Stolyarova; Arthur O Zalevsky; Dmitry Y Panteleev; Galina V Pavlova ...
 
 
Data Resources and Analyses
 
 
 
LncMAP: Pan-cancer atlas of long noncoding RNA-mediated transcriptional network perturbations border= 
 
Yongsheng Li; Lili Li; Zishan Wang; Tao Pan ; Nidhi Sahni ...
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
NRF2 regulates endothelial glycolysis and proliferation with miR-93 and mediates the effects of oxidized phospholipids on endothelial activation border= 
 
Suvi M Kuosmanen; Emilia Kansanen; Minna U Kaikkonen; Virve Sihvola; Kati Pulkkinen ...
 
 
 
 
Nuclear mRNA degradation tunes the gain of the unfolded protein response in Saccharomyces cerevisiae border= 
 
Debasish Sarkar; Sunirmal Paira; Biswadip Das
 
 
The TFIIE-related Rpc82 subunit of RNA polymerase III interacts with the TFIIB-related transcription factor Brf1 and the polymerase cleft for transcription initiation border= 
 
Seok-Kooi Khoo; Chih-Chien Wu; Yu-Chun Lin; Hung-Ta Chen
 
 
Prolyl isomerization of the CENP-A N-terminus regulates centromeric integrity in fission yeast border= 
 
Hwei Ling Tan; Kim Kiat Lim ; Qiaoyun Yang; Jing-Song Fan; Ahmed Mahmoud Mohammed Sayed ...
 
 
JUNB governs a feed-forward network of TGFbeta signaling that aggravates breast cancer invasion border= 
 
Anders Sundqvist; Masato Morikawa; Jiang Ren; Eleftheria Vasilaki ; Natsumi Kawasaki ...
 
 
Permissive zones for the centromere-binding protein ParB on the Caulobacter crescentus chromosome border= 
 
Ngat T Tran; Clare E Stevenson; Nicolle F Som; Anyarat Thanapipatsiri; Adam S B Jalal ...
 
 
Oxygen gradients can determine epigenetic asymmetry and cellular differentiation via differential regulation of Tet activity in embryonic stem cells border= 
 
Simon Burr; Anna Caldwell; Mei Chong; Matteo Beretta; Stephen Metcalf ...
 
 
Genome Integrity, Repair and Replication
 
 
 
Dormant origins and fork protection mechanisms rescue sister forks arrested by transcription border= 
 
Alessandra Brambati ; Luca Zardoni; Yathish Jagadheesh Achar; Daniele Piccini; Lorenzo Galanti ...
 
 
Enhanced spontaneous DNA twisting/bending fluctuations unveiled by fluorescence lifetime distributions promote mismatch recognition by the Rad4 nucleotide excision repair complex border= 
 
Sagnik Chakraborty ; Peter J Steinbach; Debamita Paul; Hong Mu; Suse Broyde ...
 
 
Recruitment of UvrBC complexes to UV-induced damage in the absence of UvrA increases cell survival border= 
 
Luke Springall; Craig D Hughes ; Michelle Simons; Stavros Azinas; Bennett Van Houten ...
 
 
ZNF830 mediates cancer chemoresistance through promoting homologous-recombination repair border= 
 
Guo Chen; Jianxiang Chen; Yiting Qiao; Yaru Shi ; Wei Liu ...
 
 
FANCD2 binding identifies conserved fragile sites at large transcribed genes in avian cells border= 
 
Constanze Pentzold; Shiraz Ali Shah; Niels Richard Hansen; Benoît Le Tallec; Andaine Seguin-Orlando ...
 
 
Genomics
 
 
 
Genomic basis of recombination suppression in the hybrid between Caenorhabditis briggsae and C. nigoni border= 
 
Xiaoliang Ren ; Runsheng Li; Xiaolin Wei; Yu Bi; Vincy Wing Sze Ho ...
 
 
Molecular Biology
 
 
 
Recombination directionality factor gp3 binds ¤-C31 integrase via the zinc domain, potentially affecting the trajectory of the coiled-coil motif border= 
 
Paul C M Fogg ; Ellen Younger; Booshini D Fernando; Thanafez Khaleel; W Marshall Stark ...
 
 
The effects of transcription and recombination on mutational dynamics of short tandem repeats border= 
 
Monika Zavodna; Andrew Bagshaw ; Rudiger Brauning; Neil J Gemmell
 
 
Set2 methyltransferase facilitates cell cycle progression by maintaining transcriptional fidelity border= 
 
Raghuvar Dronamraju; Deepak Kumar Jha; Umut Eser; Alexander T Adams ; Daniel Dominguez ...
 
 
The regulon of the RNA chaperone CspA and its auto-regulation in Staphylococcus aureus border= 
 
Carlos J Caballero; Pilar Menendez-Gil; Arancha Catalan-Moreno; Marta Vergara-Irigaray; Begoña García ...
 
 
Nucleic Acid Enzymes
 
 
 
Accuracy of genetic code translation and its orthogonal corruption by aminoglycosides and Mg2+ ions border= 
 
Jingji Zhang ; Michael Y Pavlov; Måns Ehrenberg
 
 
Refined sgRNA efficacy prediction improves large- and small-scale CRISPR'Cas9 applications border= 
 
Maurice Labuhn; Felix F Adams; Michelle Ng; Sabine Knoess ; Axel Schambach ...
 
 
Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: perspectives on the evolution scenario border= 
 
Charles Bou-Nader; Hugo Montémont; Vincent Guérineau; Olivier Jean-Jean; Damien Brégeon ...
 
 
Structure and mechanism of a bacterial t6A biosynthesis system border= 
 
Amit Luthra ; William Swinehart; Susan Bayooz; Phuc Phan; Boguslaw Stec ...
 
 
RNA and RNA-protein complexes
 
 
 
Dynamic m6 A modification regulates local translation of mRNA in axons border= 
 
Jun Yu; Mengxian Chen ; Haijiao Huang; Junda Zhu; Huixue Song ...
 
 
Targeted nanocomplex carrying siRNA against MALAT1 sensitizes glioblastoma to temozolomide border= 
 
Sang-Soo Kim; Joe B Harford; Manish Moghe; Antonina Rait ; Kathleen F Pirollo ...
 
 
Insights into the evolutionary conserved regulation of Rio ATPase activity border= 
 
Robert Knüppel; Regitse H Christensen; Fiona C Gray; Dominik Esser; Daniela Strauß ...
 
 
La-related protein 1 (LARP1) repression of TOP mRNA translation is mediated through its cap-binding domain and controlled by an adjacent regulatory region border= 
 
Lucas Philippe; Jean-Jacques Vasseur; Françoise Debart; Carson C Thoreen
 
 
Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa  border= 
 
Elisabeth Sonnleitner; Alexander Wulf ; Sébastien Campagne; Xue-Yuan Pei; Michael T Wolfinger ...
 
 
Structural Biology
 
 
 
Insights into the structural and mechanistic basis of multifunctional S. cerevisiae Pif1p helicase border= 
 
Ke-Yu Lu; Wei-Fei Chen ; Stephane Rety; Na-Nv Liu; Wen-Qiang Wu ...
 
 
A peculiar IclR family transcription factor regulates para-hydroxybenzoate catabolism in Streptomyces coelicolor border= 
 
Rui Zhang; Dana M Lord; Rakhi Bajaj ; Wolfgang Peti; Rebecca Page ...
 
 
Single-molecule DNA unzipping reveals asymmetric modulation of a transcription factor by its binding site sequence and context border= 
 
Sergei Rudnizky; Hadeel Khamis; Omri Malik; Allison H Squires ; Amit Meller ...
 
 
Structure and function of the N-terminal domain of the yeast telomerase reverse transcriptase border= 
 
Olga A Petrova; Alexey B Mantsyzov; Elena V Rodina; Sergey V Efimov; Claudia Hackenberg ...
 
 
Synthetic Biology and Bioengineering
 
 
 
Regulation of T cell proliferation with drug-responsive microRNA switches border= 
 
Remus S Wong ; Yvonne Y Chen; Christina D Smolke
 
 
DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size border= 
 
Dinesh C Khara; John S Schreck; Toma E Tomov; Yaron Berger ; Thomas E Ouldridge ...
 
 
Corrigendum
 
 
 
Regulation of mitotic recombination between DNA repeats in centromeres border= 
 
Faria Zafar; Akiko K Okita; Atsushi T Onaka; Jie Su; Yasuhiro Katahira ...
 
 
Methods Online
 
 
 
Site-specific dual-color labeling of long RNAs for single-molecule spectroscopy border= 
 
Meng Zhao ; Fabio D Steffen; Richard Börner; Michelle F Schaffer; Roland K O Sigel ...
 
 
A sparse differential clustering algorithm for tracing cell type changes via single-cell RNA-sequencing data border= 
 
Martin Barron; Siyuan Zhang ; Jun Li
 
 
The discovery potential of RNA processing profiles border= 
 
Amadís Pagès; Ivan Dotu; Joan Pallarès-Albanell; Eulàlia Martí; Roderic Guigó ...
 
 
TWJ-Screen: an isothermal screening assay to assess ligand/DNA junction interactions in vitro border= 
 
Ludivine Guyon ; Marc Pirrotta; Katerina Duskova; Anton Granzhan; Marie-Paule Teulade-Fichou ...
 
 
Development and application of a recombination-based library versus library high- throughput yeast two-hybrid (RLL-Y2H) screening system border= 
 
Fang Yang ; Yingying Lei; Meiling Zhou; Qili Yao; Yichao Han ...
 
 
Jointly aligning a group of DNA reads improves accuracy of identifying large deletions border= 
 
Anish M S Shrestha; Martin C Frith ; Kiyoshi Asai; Hugues Richard
 
 
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