Subject: Nucleic Acids Research Table of Contents for 19 May 2017 Oxford Academic
 
 
 
oxford_logo.jpg
 
 
 
 
New issue alert
 
Nucleic Acids Research  
Volume 45 Issue 9
 
19 May 2017
 
button-issue.png
 
 
 
 
 
 
NAR Breakthrough Article
 
 
 
The CDI toxin of Yersinia kristensenii is a novel bacterial member of the RNase A superfamily border= 
 
Ga√ęlle Batot; Karolina Michalska; Greg Ekberg; Ervin M. Irimpan ; Grazyna Joachimiak ...
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Chiral metallohelices enantioselectively target hybrid human telomeric G-quadruplex DNA border= 
 
Andong Zhao; Suzanne E. Howson; Chuanqi Zhao; Jinsong Ren ; Peter Scott ...
 
 
Pseudorotaxane formation via the slippage process with chemically cyclized oligonucleotides border= 
 
Kazumitsu Onizuka; Tomoko Chikuni; Takuya Amemiya; Takuya Miyashita; Kyoko Onizuka ...
 
 
Computational Biology
 
 
 
Enhancing identification of cancer types via lowly-expressed microRNAs border= 
 
Roni Rasnic ; Nathan Linial; Michal Linial
 
 
Data Resources and Analyses
 
 
 
A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing border= 
 
Runxuan Zhang; Cristiane P. G. Calixto; Yamile Marquez; Peter Venhuizen ; Nikoleta A. Tzioutziou ...
 
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Efficient chromosomal-scale DNA looping in Escherichia coli using multiple DNA-looping elements border= 
 
Nan Hao; Kim Sneppen; Keith E. Shearwin; Ian B. Dodd
 
 
p27Kip1, PCAF and PAX5 cooperate in the transcriptional regulation of specific target genes border= 
 
Anna Perearnau; Serena Orlando ; Abul B.M.M.K. Islam; Edurne Gallastegui; Jonatan Martínez ...
 
 
Modeling complex patterns of differential DNA methylation that associate with gene expression changes border= 
 
Christopher E. Schlosberg; Nathan D. VanderKraats; John R. Edwards
 
 
Homo-trimerization is essential for the transcription factor function of Myrf for oligodendrocyte differentiation border= 
 
Dongkyeong Kim; Jin-ok Choi; Chuandong Fan; Randall S. Shearer; Mohamed Sharif ...
 
 
Natural antisense transcripts are significantly involved in regulation of drought stress in maize border= 
 
Jie Xu; Qi Wang; Micheal Freeling; Xuecai Zhang ; Yunbi Xu ...
 
 
 
 
tRNA-derived small RNAs target transposable element transcripts border= 
 
German Martinez ; Sarah G. Choudury; R. Keith Slotkin
 
 
CTG repeat-targeting oligonucleotides for down-regulating Huntingtin expression border= 
 
Eman M. Zaghloul; Olof Gissberg; Pedro M.D. Moreno; Lee Siggens ; Mattias Hällbrink ...
 
 
TIEG1 modulates beta -catenin sub-cellular localization and enhances Wnt signaling in bone border= 
 
Malayannan Subramaniam; Muzaffer Cicek; Kevin S. Pitel; Elizabeth S. Bruinsma; Molly H. Nelson Holte ...
 
 
Gcn5-mediated Rph1 acetylation regulates its autophagic degradation under DNA damage stress border= 
 
Feng Li ; Liang-De Zheng; Xin Chen; Xiaolu Zhao; Scott D. Briggs ...
 
 
Genome Integrity, Repair and Replication
 
 
 
Highly efficient biallelic genome editing of human ES/iPS cells using a CRISPR/Cas9 or TALEN system border= 
 
Kazuo Takayama; Keisuke Igai ; Yasuko Hagihara; Rina Hashimoto; Morifumi Hanawa ...
 
 
High tolerance to self-targeting of the genome by the endogenous CRISPR-Cas system in an archaeon border= 
 
Aris-Edda Stachler; Israela Turgeman-Grott; Ella Shtifman-Segal ; Thorsten Allers; Anita Marchfelder ...
 
 
Yeast Hrq1 shares structural and functional homology with the disease-linked human RecQ4 helicase border= 
 
Cody M. Rogers; Joseph Che-Yen Wang; Hiroki Noguchi; Tsuyoshi Imasaki ; Yuichiro Takagi ...
 
 
The mechanism of the glycosylase reaction with hOGG1 base-excision repair enzyme: concerted effect of Lys249 and Asp268 during excision of 8-oxoguanine border= 
 
Jakub ҆ebera; Yoshikazu Hattori; Daichi Sato; David Ňėeha; Radim Nencka ...
 
 
Avoidance of APOBEC3B-induced mutation by error-free lesion bypass border= 
 
James I. Hoopes ; Amber L. Hughes; Lauren A. Hobson; Luis M. Cortez; Alexander J. Brown ...
 
 
Rad50 ATPase activity is regulated by DNA ends and requires coordination of both active sites border= 
 
Rajashree A. Deshpande; Ji-Hoon Lee ; Tanya T. Paull
 
 
Rgf1p (Rho1p GEF) is required for double-strand break repair in fission yeast border= 
 
Elvira Manj√≥n; Tom√°s Edreira; Sof√≠a Mu√Īoz; Yolanda S√°nchez
 
 
Genomics
 
 
 
Genomic and transcriptomic landscape of Escherichia coli BL21(DE3) border= 
 
Sinyeon Kim; Haeyoung Jeong ; Eun-Youn Kim; Jihyun F. Kim; Sang Yup Lee ...
 
 
Molecular Biology
 
 
 
Truncated ORF1 proteins can suppress LINE-1 retrotransposition in trans border=  
 
Mark Sokolowski; May Chynces; Dawn deHaro ; Claiborne M. Christian; Victoria P. Belancio
 
 
Intra-endosomal trafficking mediated by lysobisphosphatidic acid contributes to intracellular release of phosphorothioate-modified antisense oligonucleotides border= 
 
Shiyu Wang; Hong Sun; Michael Tanowitz; Xue-hai Liang ; Stanley T. Crooke
 
 
Nucleic Acid Enzymes
 
 
 
High pressure activation of the Mrr restriction endonuclease in Escherichia coli involves tetramer dissociation border= 
 
Ana√Įs C. Bourges; Oscar E. Torres Montaguth; Anirban Ghosh; Wubishet M. Tadesse; Nathalie Declerck ...
 
 
Substrate preference of Gen endonucleases highlights the importance of branched structures as DNA damage repair intermediates border= 
 
Stephanie P. Bellendir; Danielle J. Rognstad; Lydia P. Morris; Grzegorz Zapotoczny; William G. Walton ...
 
 
Deacetylation of topoisomerase I is an important physiological function of E. coli CobB border= 
 
Qingxuan Zhou; Yan Ning Zhou ; Ding Jun Jin; Yuk-Ching Tse-Dinh
 
 
RNA
 
 
 
The G-patch protein NF-kappa B-repressing factor mediates the recruitment of the exonuclease XRN2 and activation of the RNA helicase DHX15 in human ribosome biogenesis border= 
 
Indira Memet; Carmen Doebele; Katherine E. Sloan; Markus T. Bohnsack
 
 
Ligand binding to 2ő"-deoxyguanosine sensing riboswitch in metabolic context border= 
 
Yong-Boum Kim; Anna Wacker ; Karl von Laer; Vladimir V. Rogov; Beatrix Suess ...
 
 
Roles of MIWI, MILI and PLD6 in small RNA regulation in mouse growing oocytes border= 
 
Yuka Kabayama; Hidehiro Toh; Ami Katanaya; Takayuki Sakurai ; Shinichiro Chuma ...
 
 
SECIS-binding protein 2 interacts with the SMN complex and the methylosome for selenoprotein mRNP assembly and translation border= 
 
Anne-Sophie Gribling-Burrer; Michael Leichter; Laurence Wurth; Alexandra Huttin; Florence Schlotter ...
 
 
Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction border= 
 
Cigdem Sevim Bayrak ; Namhee Kim; Tamar Schlick
 
 
Human BCDIN3D monomethylates cytoplasmic histidine transfer RNA border= 
 
Anna Martinez; Seisuke Yamashita; Takashi Nagaike; Yuriko Sakaguchi; Tsutomu Suzuki ...
 
 
Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences border= 
 
Amin Espah Borujeni; Daniel Cetnar; Iman Farasat; Ashlee Smith; Natasha Lundgren ...
 
 
Self-assembly of multi-stranded RNA motifs into lattices and tubular structures border= 
 
Jaimie Marie Stewart; Hari K. K. Subramanian ; Elisa Franco
 
 
The lncRNA VELUCT strongly regulates viability of lung cancer cells despite its extremely low abundance border= 
 
Jana Seiler; Marco Breinig; Ma√Įwen Caudron-Herger; Maria Polycarpou-Schwarz; Michael Boutros ...
 
 
A transposon-derived small RNA regulates gene expression in Salmonella Typhimurium border= 
 
Michael J. Ellis ; Ryan S. Trussler; Onella Charles; David B. Haniford
 
 
Simultaneous processing and degradation of mitochondrial RNAs revealed by circularized RNA sequencing border= 
 
Irina Kuznetsova; Stefan J. Siira; Anne-Marie J. Shearwood; Judith A. Ermer; Aleksandra Filipovska ...
 
 
Characterization of human telomere RNA G-quadruplex structures in vitro and in living cells using 19F NMR spectroscopy border= 
 
Hong-Liang Bao; Takumi Ishizuka; Takashi Sakamoto; Kenzo Fujimoto; Tamayo Uechi ...
 
 
Ligand-modulated folding of the full-length adenine riboswitch probed by NMR and single-molecule FRET spectroscopy border= 
 
Sven Warhaut ; Klara Rebecca Mertinkus; Philipp H√∂llthaler; Boris F√ľrtig; Mike Heilemann ...
 
 
Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions border= 
 
Jorge Vazquez-Anderson; Mia K. Mihailovic; Kevin C. Baldridge; Kristofer G. Reyes; Katie Haning ...
 
 
A single miR390 targeting event is sufficient for triggering TAS3-tasiRNA biogenesis in Arabidopsis border=  
 
Felipe Fenselau de Felippes; Antonin Marchais; Alexis Sarazin ; Stefan Oberlin; Olivier Voinnet
 
 
Structural Biology
 
 
 
Crystal structure of the N-terminal domain of human Timeless and its interaction with Tipin border= 
 
Sandro Holzer; Gianluca Degliesposti; Mairi L. Kilkenny; Sarah L. Maslen ; Dijana Matak-Vinkovíc ...
 
 
Structural characterization of interactions between transactivation domain 1 of the p65 subunit of NF-kappa B and transcription regulatory factors border= 
 
Lauriane Lecoq; Luca Raiola; Philippe R. Chabot; Normand Cyr; Geneviève Arseneault ...
 
 
Structure of the Sac3 RNA-binding M-region in the Saccharomyces cerevisiae TREX-2 complex border= 
 
James M. B. Gordon ; Shintaro Aibara; Murray Stewart
 
 
Insights into Watson'Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A border= 
 
Bharathwaj Sathyamoorthy; Honglue Shi; Huiqing Zhou; Yi Xue ; Atul Rangadurai ...
 
 
NMR-based method of small changes reveals how DNA mutator APOBEC3A interacts with its single-stranded DNA substrate border= 
 
Stefan Harjes; Geoffrey B. Jameson; Vyacheslav V. Filichev; Patrick J. B. Edwards; Elena Harjes
 
 
Synthetic Biology and Bioengineering
 
 
 
Achieving large dynamic range control of gene expression with a compact RNA transcription'translation regulator border= 
 
Alexandra M. Westbrook ; Julius B. Lucks
 
 
Corrigendum
 
 
 
ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium border= 
 
Qi You; Wenying Xu; Kang Zhang; Liwei Zhang; Xin Yi ...
 
 
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes 
 
Michael Y. Galperin; Xosé M. Fernández-Suárez; Daniel J. Rigden
 
 
Self-assembly of multi-stranded RNA motifs into lattices and tubular structures border= 
 
Jaimie Marie Stewart ; Hari K.K. Subramanian; Elisa Franco
 
 
Methods Online
 
 
 
Visualizing single-stranded nucleic acids in solution border= 
 
Alex Plumridge; Steve P. Meisburger; Lois Pollack
 
 
PBrowse: a web-based platform for real-time collaborative exploration of genomic data border= 
 
Peter S. Szot; Andrian Yang ; Xin Wang; Chirag Parsania; Uwe Röhm ...
 
 
Amplification of unscheduled DNA synthesis signal enables fluorescence-based single cell quantification of transcription-coupled nucleotide excision repair border=  
 
Franziska Wienholz; Wim Vermeulen; Jurgen A. Marteijn
 
 
Computational approach for deriving cancer progression roadmaps from static sample data border= 
 
Yijun Sun; Jin Yao ; Le Yang; Runpu Chen; Norma J. Nowak ...
 
 
YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs border= 
 
Megumi Shigematsu; Shozo Honda; Phillipe Loher; Aristeidis G. Telonis ; Isidore Rigoutsos ...
 
 
From benchmarking HITS-CLIP peak detection programs to a new method for identification of miRNA-binding sites from Ago2-CLIP data border= 
 
Silvia Bottini; Nedra Hamouda-Tekaya; Bogdan Tanasa; Laure-Emmanuelle Zaragosi; Valerie Grandjean ...
 
 
digit'a tool for detection and identification of genomic interchromosomal translocations border= 
 
Richard Meier; Stefan Graw; Peter Beyerlein; Devin Koestler; Julian R. Molina ...
 
 
High-throughput single-molecule mapping links subtelomeric variants and long-range haplotypes with specific telomeres border= 
 
Eleanor Young; Steven Pastor; Ramakrishnan Rajagopalan; Jennifer McCaffrey; Justin Sibert ...
 
 
The CCTL (Cpf1-assisted Cutting and Taq DNA ligase-assisted Ligation) method for efficient editing of large DNA constructs in vitro  border= 
 
Chao Lei; Shi-Yuan Li ; Jia-Kun Liu; Xuan Zheng; Guo-Ping Zhao ...
 
 
Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework border= 
 
Miaoxin Li; Jiang Li; Mulin Jun Li; Zhicheng Pan; Jacob Shujui Hsu ...
 
 
Unsubscribe       Manage email alerts
 
Written requests to unsubscribe can be sent to: Journals Marketing, Oxford University Press, Great Clarendon Street, Oxford, OX2 6DP, UK.

The content of this email is protected by copyright.
 
oxforde_university.jpg
 
 
 
                                 


This email is intended for bionet@evol.biology.mcmaster.ca.