Subject: Nucleic Acids Research Table of Contents for 20 April 2018 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Nucleic Acids Research  
Volume 46 Issue 7
 
20 April 2018
 
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NAR Breakthrough Article
 
 
 
An interplay of miRNA abundance and target site architecture determines miRNA activity and specificity border= 
 
Giovanna Brancati; Helge Großhans
 
 
SURVEY AND SUMMARY
 
 
 
G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy border=  
 
Emanuela Ruggiero; Sara N Richter
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
ZYH005, a novel DNA intercalator, overcomes all-trans retinoic acid resistance in acute promyelocytic leukemia border= 
 
Qingyi Tong; Huijuan You; Xintao Chen; Kongchao Wang; Weiguang Sun ...
 
 
Computational Biology
 
 
 
Structural changes in DNA-binding proteins on complexation border=  
 
Sayan Poddar; Devlina Chakravarty; Pinak Chakrabarti
 
 
ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer border= 
 
Nam-phuong D Nguyen ; Viraj Deshpande; Jens Luebeck; Paul S Mischel; Vineet Bafna
 
 
 
 
A comprehensive catalog of predicted functional upstream open reading frames in humans border=  
 
Patrick McGillivray; Russell Ault; Mayur Pawashe ; Robert Kitchen; Suganthi Balasubramanian ...
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Regulation of the positive transcriptional effect of PLZF through a non-canonical EZH2 activity border=  
 
Myriam Koubi; Mathilde Poplineau; Julien Vernerey ; Lia N'Guyen; Guillaume Tiberi ...
 
 
Lineage specific transcription factors and epigenetic regulators mediate TGFbeta -dependent enhancer activation border= 
 
Raquel Fueyo; Simona Iacobucci; Stella Pappa; Conchi Estarás ; Sergio Lois ...
 
 
An RNA-dependent mechanism for transient expression of bacterial translocation filaments border= 
 
Dai Wang; Sean P McAteer; Agata B Wawszczyk; Clark D Russell; Amin Tahoun ...
 
 
Ezh2 promotes clock function and hematopoiesis independent of histone methyltransferase activity in zebrafish border= 
 
Yingbin Zhong ; Qiang Ye; Chengyan Chen; Mingyong Wang; Han Wang
 
 
 
 
Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli border=  
 
Nalini Raghunathan; Rajvardhan M Kapshikar; Jakku K Leela ; Jillella Mallikarjun; Philippe Bouloc ...
 
 
Combined cistrome and transcriptome analysis of SKI in AML cells identifies SKI as a co-repressor for RUNX1 border= 
 
Christine Feld; Peeyush Sahu; Miriam Frech; Florian Finkernagel ; Andrea Nist ...
 
 
N4-cytosine DNA methylation regulates transcription and pathogenesis in Helicobacter pylori border= 
 
Sumith Kumar; Bipul C Karmakar; Deepesh Nagarajan; Asish K Mukhopadhyay; Richard D Morgan ...
 
 
Genome Integrity, Repair and Replication
 
 
 
Super-resolution imaging identifies PARP1 and the Ku complex acting as DNA double-strand break sensors border= 
 
Guang Yang ; Chao Liu; Shih-Hsun Chen; Muzaffer A Kassab; J Damon Hoff ...
 
 
Oxidative stress increases M1 dG, a major peroxidation-derived DNA adduct, in mitochondrial DNA border= 
 
Orrette R Wauchope; Michelle M Mitchener ; William N Beavers; James J Galligan; Jeannie M Camarillo ...
 
 
Pold3 is required for genomic stability and telomere integrity in embryonic stem cells and meiosis border=  
 
Zhongcheng Zhou; Lingling Wang; Feixiang Ge ; Peng Gong; Hua Wang ...
 
 
RNA'DNA hybrids promote the expansion of Friedreich's ataxia (GAA)n repeats via break-induced replication border= 
 
Alexander J Neil; Miranda U Liang; Alexandra N Khristich; Kartik A Shah ; Sergei M Mirkin
 
 
Genetic instability associated with loop or stem'loop structures within transcription units can be independent of nucleotide excision repair border= 
 
John A Burns; Moinuddin A Chowdhury; Laura Cartularo; Christian Berens; David A Scicchitano
 
 
Genomics
 
 
 
A screen for deeply conserved non-coding GWAS SNPs uncovers a MIR-9-2 functional mutation associated to retinal vasculature defects in human border= 
 
Romain Madelaine; James H Notwell; Gemini Skariah; Caroline Halluin; Charles C Chen ...
 
 
A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase-variable regulons; phasevarions border= 
 
John M Atack; Yuedong Yang; Kate L Seib; Yaoqi Zhou; Michael P Jennings
 
 
Molecular Biology
 
 
 
DNA as UV light'harvesting antenna border= 
 
Ivan L Volkov ; Zakhar V Reveguk; Pavel Yu Serdobintsev; Ruslan R Ramazanov; Alexei I Kononov
 
 
The yeast Ty1 retrotransposon requires components of the nuclear pore complex for transcription and genomic integration border= 
 
Savrina Manhas ; Lina Ma; Vivien Measday
 
 
Cellular uptake mediated by epidermal growth factor receptor facilitates the intracellular activity of phosphorothioate-modified antisense oligonucleotides border= 
 
Shiyu Wang; Nickolas Allen; Timothy A Vickers; Alexey S Revenko ; Hong Sun ...
 
 
HpoR, a novel c-di-GMP effective transcription factor, links the second messenger's regulatory function to the mycobacterial antioxidant defense border= 
 
Weihui Li; Meng Li; Lihua Hu; Jingpeng Zhu; Zhiwei Xie ...
 
 
Ammonium and arsenic trioxide are potent facilitators of oligonucleotide function when delivered by gymnosis border= 
 
Xiaowei Zhang ; Daniela Castanotto; Xueli Liu; Amotz Shemi; Cy A Stein
 
 
Nucleic Acid Enzymes
 
 
 
Limited reverse transcriptase activity of phi29 DNA polymerase border= 
 
Tomasz Krzywkowski; Malte Kühnemund ; Di Wu; Mats Nilsson
 
 
Acetylation and phosphorylation of human TFAM regulate TFAM'DNA interactions via contrasting mechanisms border= 
 
Graeme A King; Maryam Hashemi Shabestari; Kees-Karel H Taris; Ashutosh K Pandey ; Sundararajan Venkatesh ...
 
 
A threonyl-tRNA synthetase-like protein has tRNA aminoacylation and editing activities border= 
 
Yun Chen; Zhi-Rong Ruan; Yong Wang; Qian Huang; Mei-Qin Xue ...
 
 
RNA and RNA-protein complexes
 
 
 
Structural divergence creates new functional features in alphavirus genomes border= 
 
Katrina M Kutchko ; Emily A Madden; Clayton Morrison; Kenneth S Plante; Wes Sanders ...
 
 
Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis -backsplicing in human cells border= 
 
Trees-Juen Chuang; Yen-Ju Chen ; Chia-Ying Chen; Te-Lun Mai; Yi-Da Wang ...
 
 
Maturation of the 90S pre-ribosome requires Mrd1 dependent U3 snoRNA and 35S pre-rRNA structural rearrangements border= 
 
Fredrik Lackmann; Sergey Belikov; Elena Burlacu ; Sander Granneman; Lars Wieslander
 
 
Pumilio directs deadenylation-associated translational repression of the cyclin-dependent kinase 1 activator RGC-32 border= 
 
Michèle Brocard; Sarika Khasnis; C David Wood; Claire Shannon-Lowe ; Michelle J West
 
 
Dicer partner protein tunes the length of miRNAs using base-mismatch in the pre-miRNA stem border= 
 
Li Zhu; Suresh K Kandasamy; Ryuya Fukunaga
 
 
Structural analyses of NEAT1 lncRNAs suggest long-range RNA interactions that may contribute to paraspeckle architecture border= 
 
Yizhu Lin; Brigitte F Schmidt; Marcel P Bruchez ; C Joel McManus
 
 
Antibiotic resistance ABCF proteins reset the peptidyl transferase centre of the ribosome to counter translational arrest border= 
 
Victoriia Murina; Marje Kasari; Vasili Hauryliuk; Gemma C Atkinson
 
 
The Sm-core mediates the retention of partially-assembled spliceosomal snRNPs in Cajal bodies until their full maturation border= 
 
Adriana Roithová ; Klára KlimeÅ¡ová; Josef Pánek; Cindy L Will; Reinhard Lührmann ...
 
 
Structural Biology
 
 
 
Structural basis for LeishIF4E-1 modulation by an interacting protein in the human parasite Leishmania major border= 
 
Shimi Meleppattu ; Haribabu Arthanari; Alexandra Zinoviev; Andras Boeszoermenyi; Gerhard Wagner ...
 
 
The structure of the RbBP5 beta -propeller domain reveals a surface with potential nucleic acid binding sites border= 
 
Anshumali Mittal; Fruzsina Hobor; Ying Zhang; Stephen R Martin; Steven J Gamblin ...
 
 
Corrigendum
 
 
 
Rapid decay of engulfed extracellular miRNA by XRN1 exonuclease promotes transient epithelial-mesenchymal transition border= 
 
Joséphine Zangari ; Marius Ilie; Florian Rouaud; Laurie Signetti; Mickaël Ohanna ...
 
 
Erratum
 
 
 
N4-cytosine DNA methylation regulates transcription and pathogenesis in Helicobacter pylori border= 
 
Sumith Kumar; Bipul C Karmakar ; Deepesh Nagarajan; Asish K Mukhopadhyay; Richard D Morgan ...
 
 
Methods Online
 
 
 
Selective terminal methylation of a tRNA wobble base border=  
 
Isao Masuda; Ryuichi Takase; Ryuma Matsubara ; Mellie June Paulines; Howard Gamper ...
 
 
Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D border= 
 
Piroon Jenjaroenpun; Thidathip Wongsurawat; Rui Pereira; Preecha Patumcharoenpol ; David W Ussery ...
 
 
RGBM: regularized gradient boosting machines for identification of the transcriptional regulators of discrete glioma subtypes border= 
 
Raghvendra Mall; Luigi Cerulo; Luciano Garofano; Veronique Frattini; Khalid Kunji ...
 
 
Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms border= 
 
Hyeonseob Lim; Namjin Cho; Jinwoo Ahn; Sangun Park; Hoon Jang ...
 
 
A rapid fluorescent indicator displacement assay and principal component/cluster data analysis for determination of ligand'nucleic acid structural selectivity border= 
 
Rafael del Villar-Guerra; Robert D Gray; John O Trent; Jonathan B Chaires
 
 
Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery border= 
 
Dimitra Aggeli; Vlad O Karas; Nicholas A Sinnott-Armstrong; Vici Varghese; Robert W Shafer ...
 
 
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