Subject: Nucleic Acids Research Table of Contents for 28 February 2018 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Nucleic Acids Research  
Volume 46 Issue 4
 
28 February 2018
 
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Editorial
 
 
 
Editorial: Nucleic Acids Research and Nucleic Acid Therapeutics border= 
 
Barry L Stoddard; Anastasia Khvorova; David R Corey; William S Dynan ; Keith R Fox
 
 
NAR Breakthrough Article
 
 
 
Metabolic and chemical regulation of tRNA modification associated with taurine deficiency and human disease border= 
 
Kana Asano; Takeo Suzuki; Ayaka Saito; Fan-Yan Wei; Yoshiho Ikeuchi ...
 
 
SURVEY AND SUMMARY
 
 
 
Chemistry, mechanism and clinical status of antisense oligonucleotides and duplex RNAs border= 
 
Xiulong Shen ; David R Corey
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Structure'activity relationships and cellular mechanism of action of small molecules that enhance the delivery of oligonucleotides border= 
 
Rudolph L Juliano; Ling Wang; Francis Tavares; Edward G Brown; Lindsey James ...
 
 
Structural properties and gene-silencing activity of chemically modified DNA'RNA hybrids with parallel orientation border= 
 
Maryam Habibian ; Maryam Yahyaee-Anzahaee; Matije Lucic; Elena Moroz; Nerea Martín-Pintado ...
 
 
 
 
i-Motif of cytosine-rich human telomere DNA fragments containing natural base lesions border= 
 
Zuzana Dvořáková; Daniel Renčiuk; Iva Kejnovská; Petra Školáková; Klára Bednářová ...
 
 
Systematic editing of synthetic RIG-I ligands to produce effective antiviral and anti-tumor RNA immunotherapies border= 
 
Janghyun Lee; Eun-Byeol Park; Jiyoun Min; Si-Eun Sung; Yejin Jang ...
 
 
Computational Biology
 
 
 
Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes border= 
 
Dusan Racko ; Fabrizio Benedetti; Julien Dorier; Andrzej Stasiak
 
 
A survey of localized sequence rearrangements in human DNA border= 
 
Martin C Frith; Sofia Khan
 
 
A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs border= 
 
Simón Poblete; Sandro Bottaro; Giovanni Bussi
 
 
 
 
Sequence-dependent response of DNA to torsional stress: a potential biological regulation mechanism border= 
 
Anna Reymer; Krystyna Zakrzewska; Richard Lavery
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
An RNA polymerase II-associated TFIIF-like complex is indispensable for SL RNA gene transcription in Trypanosoma brucei border= 
 
Ankita Srivastava; Nitika Badjatia; Ju Huck Lee; Bing Hao ; Arthur Günzl
 
 
BmILF and i-motif structure are involved in transcriptional regulation of BmPOUM2 in Bombyx mori border= 
 
Kangkang Niu; Xiaojuan Zhang; Huimin Deng; Feng Wu; Yandong Ren ...
 
 
Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions border= 
 
Henri Niskanen; Irina Tuszynska; Rafal Zaborowski; Merja Heinäniemi; Seppo Ylä-Herttuala ...
 
 
Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein border= 
 
Yogambigai Velmurugu ; Paula Vivas; Mitchell Connolly; Serguei V Kuznetsov; Phoebe A Rice ...
 
 
Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers border= 
 
Gilson J Sanchez ; Phillip A Richmond; Eric N Bunker; Samuel S Karman; Joseph Azofeifa ...
 
 
Spliceosomal protein U1A is involved in alternative splicing and salt stress tolerance in Arabidopsis thaliana  border= 
 
Jinbao Gu; Zhiqiang Xia ; Yuehua Luo; Xingyu Jiang; Bilian Qian ...
 
 
The interaction of lncRNA EZR-AS1 with SMYD3 maintains overexpression of EZR in ESCC cells border= 
 
Xiao-Dan Zhang; Guo-Wei Huang; Ying-Hua Xie ; Jian-Zhong He; Jin-Cheng Guo ...
 
 
Genome Integrity, Repair and Replication
 
 
 
Bacterial artificial chromosomes establish replication timing and sub-nuclear compartment de novo as extra-chromosomal vectors border= 
 
Jiao Sima; Daniel A Bartlett; Molly R Gordon; David M Gilbert
 
 
Direct observation of end resection by RecBCD during double-stranded DNA break repair in vivo border= 
 
Jakub Wiktor ; Marit van der Does; Lisa Büller; David J Sherratt; Cees Dekker
 
 
Sp1 phosphorylation by ATM downregulates BER and promotes cell elimination in response to persistent DNA damage border= 
 
Sally C Fletcher; Claudia P Grou; Arnaud J Legrand; Xin Chen; Kalle Soderstrom ...
 
 
PIDD mediates the association of DNA-PKcs and ATR at stalled replication forks to facilitate the ATR signaling pathway border=  
 
Yu-Fen Lin; Hung-Ying Shih; Zeng-Fu Shang ; Ching-Te Kuo; Jiaming Guo ...
 
 
Genomics
 
 
 
Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve border= 
 
Francesca Bottacini; Ruth Morrissey; Richard John Roberts; Kieran James ; Justin van Breen ...
 
 
Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse border= 
 
Adam G Diehl; Alan P Boyle
 
 
Molecular Biology
 
 
 
Androgen receptor splice variants bind to constitutively open chromatin and promote abiraterone-resistant growth of prostate cancer border= 
 
Yundong He; Ji Lu; Zhenqing Ye; Siyuan Hao ; Liewei Wang ...
 
 
Interplay between RNASEH2 and MOV10 controls LINE-1 retrotransposition border= 
 
Jongsu Choi; Sung-Yeon Hwang; Kwangseog Ahn
 
 
Eukaryotic translational termination efficiency is influenced by the 3 nucleotides within the ribosomal mRNA channel border= 
 
Andrew G Cridge; Caillan Crowe-McAuliffe; Suneeth F Mathew ; Warren P Tate
 
 
Nucleic Acid Enzymes
 
 
 
Oxidative stress damages rRNA inside the ribosome and differentially affects the catalytic center border= 
 
Jessica Willi; Pascal Küpfer; Damien Evéquoz; Guillermo Fernandez; Assaf Katz ...
 
 
The RNA-splicing endonuclease from the euryarchaeaon Methanopyrus kandleri is a heterotetramer with constrained substrate specificity border= 
 
Ayano Kaneta; Kosuke Fujishima; Wataru Morikazu; Hiroyuki Hori; Akira Hirata
 
 
The ribosomal A-site finger is crucial for binding and activation of the stringent factor RelA border= 
 
Pavel Kudrin ; Ievgen Dzhygyr; Kensuke Ishiguro; Jelena Beljantseva; Elena Maksimova ...
 
 
Distinct and redundant functions of three homologs of RNase III in the cyanobacterium Synechococcus sp. strain PCC 7002 border= 
 
Gina C Gordon; Jeffrey C Cameron ; Brian F Pfleger
 
 
RNA and RNA-protein complexes
 
 
 
A FTH1 gene:pseudogene:microRNA network regulates tumorigenesis in prostate cancer border= 
 
Jia Jia Chan; Zhi Hao Kwok; Xiao Hong Chew; Bin Zhang ; Chao Liu ...
 
 
Nuclear miR-122 directly regulates the biogenesis of cell survival oncomiR miR-21 at the posttranscriptional level border= 
 
Dong Wang; Xinlei Sun; Yao Wei; Hongwei Liang; Min Yuan ...
 
 
PolyC-binding proteins enhance expression of the CDK2 cell cycle regulatory protein via alternative splicing border= 
 
Xinjun Ji ; Jesse Humenik; Daphne Yang; Stephen A Liebhaber
 
 
ADAR2/miR-589-3p axis controls glioblastoma cell migration/invasion border= 
 
Valeriana Cesarini; Domenico A Silvestris; Valentina Tassinari ; Sara Tomaselli; Shahar Alon ...
 
 
Directed hydroxyl radical probing reveals Upf1 binding to the 80S ribosomal E site rRNA at the L1 stalk border= 
 
Anthony P Schuller; Boris Zinshteyn; Syed Usman Enam; Rachel Green
 
 
Structural Biology
 
 
 
How does temperature impact the conformation of single DNA molecules below melting temperature? border= 
 
Annaël Brunet ; Laurence Salomé; Philippe Rousseau; Nicolas Destainville; Manoel Manghi ...
 
 
Structural basis of gene regulation by the Grainyhead/CP2 transcription factor family border= 
 
Qianqian Ming; Yvette Roske ; Anja Schuetz; Katharina Walentin; Ibraim Ibraimi ...
 
 
Structural and functional analysis of ribosome assembly factor Efg1 border= 
 
Sheng Shu; Keqiong Ye
 
 
The C-terminal region of translesion synthesis DNA polymerase eta is partially unstructured and has high conformational flexibility border=  
 
Kyle T Powers; Adrian H Elcock; M Todd Washington
 
 
Synthetic Biology and Bioengineering
 
 
 
Riboswitching with ciprofloxacin'development and characterization of a novel RNA regulator border= 
 
Florian Groher ; Cristina Bofill-Bosch; Christopher Schneider; Johannes Braun; Sven Jager ...
 
 
A sigma factor toolbox for orthogonal gene expression in Escherichia coli  border= 
 
Indra Bervoets; Maarten Van Brempt ; Katleen Van Nerom; Bob Van Hove; Jo Maertens ...
 
 
Methods Online
 
 
 
Identification of large rearrangements in cancer genomes with barcode linked reads border=  
 
Li C Xia; John M Bell; Christina Wood-Bouwens ; Jiamin J Chen; Nancy R Zhang ...
 
 
PaSD-qc: quality control for single cell whole-genome sequencing data using power spectral density estimation border= 
 
Maxwell A Sherman; Alison R Barton; Michael A Lodato; Carl Vitzthum ; Michael E Coulter ...
 
 
SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing border= 
 
Nicholas J Hathaway; Christian M Parobek; Jonathan J Juliano; Jeffrey A Bailey
 
 
Efficient in situ barcode sequencing using padlock probe-based BaristaSeq border= 
 
Xiaoyin Chen; Yu-Chi Sun ; George M Church; Je Hyuk Lee; Anthony M Zador
 
 
Functional sequencing read annotation for high precision microbiome analysis border= 
 
Chengsheng Zhu; Maximilian Miller; Srinayani Marpaka; Pavel Vaysberg; Malte C Rühlemann ...
 
 
DNA terminal structure-mediated enzymatic reaction for ultra-sensitive discrimination of single nucleotide variations in circulating cell-free DNA border= 
 
Tongbo Wu; Wei Chen; Ziyu Yang; Haocheng Tan; Jiayu Wang ...
 
 
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