Subject: Nucleic Acids Research Table of Contents for 28 February 2017 Oxford Academic
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Nucleic Acids Research  
Volume 45 Issue 4
28 February 2017
NAR Breakthrough Article
Non-canonical targets destabilize microRNAs in human Argonautes border= 
June Hyun Park; Sang-Yoon Shin; Chanseok Shin
RNA G-quadruplexes: emerging mechanisms in disease border= 
Anne Cammas; Stefania Millevoi
Counting the ions surrounding nucleic acids border= 
David R. Jacobson ; Omar A. Saleh
Chemical Biology and Nucleic Acid Chemistry
Specific targeting of telomeric multimeric G-quadruplexes by a new triaryl-substituted imidazole border= 
Ming-Hao Hu; Shuo-Bin Chen; Bo Wang; Tian-Miao Ou; Lian-Quan Gu ...
Mapping the affinity landscape of Thrombin-binding aptamers on 2Î"F-ANA/DNA chimeric G-Quadruplex microarrays border= 
Jory Lietard ; Hala Abou Assi; Irene GĂłmez-Pinto; Carlos González; Mark M. Somoza ...
Computational Biology
Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort border= 
Tomasz Gambin; Zeynep C. Akdemir ; Bo Yuan; Shen Gu; Theodore Chiang ...
k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets border= 
David Ainsworth; Michael J.E. Sternberg; Come Raczy ; Sarah A. Butcher
Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states border= 
Yang Yang; Yu-Cheng T. Yang; Jiapei Yuan; Zhi John Lu; Jingyi Jessica Li
Data Resources and Analyses
Integrative FourD omics approach profiles the target network of the carbon storage regulatory system border= 
Steven W. Sowa ; Grant Gelderman; Abigail N. Leistra; Aishwarya Buvanendiran; Sarah Lipp ...
Gene Regulation, Chromatin and Epigenetics
Histone demethylase PHF8 promotes epithelial to mesenchymal transition and breast tumorigenesis border= 
Peng Shao; Qi Liu ; Peterson Kariuki Maina; Jiayue Cui; Thomas B. Bair ...
Efficient targeted DNA methylation with chimeric dCas9'Dnmt3a'Dnmt3L methyltransferase border= 
Peter Stepper; Goran Kungulovski; Renata Z. Jurkowska; Tamir Chandra ; Felix Krueger ...
Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture border= 
Caelin Cubeñas-Potts; M. Jordan Rowley; Xiaowen Lyu; Ge Li; Elissa P. Lei ...
The adenovirus L4-22K protein regulates transcription and RNA splicing via a sequence-specific single-stranded RNA binding border= 
Susan Lan ; Wael Kamel; Tanel Punga; Göran Akusjärvi
The KDM5 family is required for activation of pro-proliferative cell cycle genes during adipocyte differentiation border= 
Ann-Sofie B. Brier; Anne Loft; Jesper G. S. Madsen ; Thomas Rosengren; Ronni Nielsen ...
Autoregulation of MBNL1 function by exon 1 exclusion from MBNL1 transcript border= 
Patryk Konieczny; Ewa Stepniak-Konieczna; Katarzyna Taylor; Ĺ ukasz J. Sznajder ; Krzysztof Sobczak
ING1 regulates rRNA levels by altering nucleolar chromatin structure and mTOR localization border= 
Uma Karthika Rajarajacholan; Subhash Thalappilly; Karl Riabowol
Identification of a novel K311 ubiquitination site critical for androgen receptor transcriptional activity border= 
Urszula L. McClurg; David M.W. Cork; Steven Darby; Claudia A. Ryan-Munden; Sirintra Nakjang ...
Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation border= 
Michael I. Love; Matthew R. Huska; Marcel Jurk; Robert Schöpflin; Stephan R. Starick ...
Genome Integrity, Repair and Replication
SIRT6 interacts with TRF2 and promotes its degradation in response to DNA damage border= 
Angela Rizzo ; Sara Iachettini; Erica Salvati; Pasquale Zizza; Carmen Maresca ...
The homologous recombination protein RAD51D protects the genome from large deletions border= 
Wade A. Reh; Rodney S. Nairn ; Megan P. Lowery; Karen M. Vasquez
SFPQ˘NONO and XLF function separately and together to promote DNA double-strand break repair via canonical nonhomologous end joining border= 
Lahcen Jaafar; Zhentian Li; Shuyi Li; William S. Dynan
RMI1 and TOP3alpha limit meiotic CO formation through their C-terminal domains border= 
Mathilde Séguéla-Arnaud; Sandrine Choinard ; Cécile Larchevêque; Chloé Girard; Nicole Froger ...
Bridging of double-stranded breaks by the nonhomologous end-joining ligation complex is modulated by DNA end chemistry border= 
Dylan A. Reid; Michael P. Conlin; Yandong Yin ; Howard H. Chang; Go Watanabe ...
Homologous recombination in budding yeast expressing the human RAD52 gene reveals a Rad51-independent mechanism of conservative double-strand break repair border= 
Glenn M. Manthey; Alissa D. Clear; Lauren C. Liddell; Maria C. Negritto ; Adam M. Bailis
Extreme mutation bias and high AT content in Plasmodium falciparum border= 
William L. Hamilton; Antoine Claessens; Thomas D. Otto; Mihir Kekre; Rick M. Fairhurst ...
Molecular Biology
CRISPR-Cas type I-A Cascade complex couples viral infection surveillance to host transcriptional regulation in the dependence of Csa3b border= 
Fei He ; Gisle Vestergaard; Wenfang Peng; Qunxin She; Xu Peng
Antibacterial and antivirulence effect of 6-N-hydroxylaminopurine in Listeria monocytogenes  border= 
Stefanie Sandra Krajewski; Isabelle Isoz ; Jörgen Johansson
FACT is a sensor of DNA torsional stress in eukaryotic cells border= 
Alfiya Safina; Peter Cheney; Mahadeb Pal; Leonid Brodsky; Alexander Ivanov ...
The action of Escherichia coli CRISPR'Cas system on lytic bacteriophages with different lifestyles and development strategies border= 
Alexandra Strotskaya; Ekaterina Savitskaya; Anastasia Metlitskaya; Natalia Morozova; Kirill A. Datsenko ...
Nucleic Acid Enzymes
DNA polymerase beta contains a functional nuclear localization signal at its N-terminus border= 
Thomas W. Kirby; Natalie R. Gassman ; Cassandra E. Smith; Ming-Lang Zhao; Julie K. Horton ...
Activation mode of the eukaryotic m2G10 tRNA methyltransferase Trm11 by its partner protein Trm112 border= 
Gabrielle Bourgeois; Julien Marcoux; Jean-Michel Saliou ; Sarah Cianférani; Marc Graille
A type III-B CRISPR-Cas effector complex mediating massive target DNA destruction border= 
Wenyuan Han; Yingjun Li; Ling Deng; Mingxia Feng ; Wenfang Peng ...
Allosteric regulation of helicase core activities of the DEAD-box helicase YxiN by RNA binding to its RNA recognition motif border= 
Brighton Samatanga; Alexandra Z. Andreou; Dagmar Klostermeier
Bypassing rRNA methylation by RsmA/Dim1during ribosome maturation in the hyperthermophilic archaeon Nanoarchaeum equitans border= 
Kenneth H. Seistrup; Simon Rose; Ulf Birkedal ; Henrik Nielsen; Harald Huber ...
Unusual CÎ"/DÎ" motifs enable box C/D snoRNPs to modify multiple sites in the same rRNA target region border= 
Robert Willem van Nues; Nicholas James Watkins
In vivo modification of tRNA with an artificial nucleobase leads to full disease remission in an animal model of multiple sclerosis border=  
Sreeja Varghese; Michelle Cotter; Franciane Chevot ; Claire Fergus; Colm Cunningham ...
Two highly conserved features of bacterial initiator tRNAs license them to pass through distinct checkpoints in translation initiation border= 
Sunil Shetty; Riyaz A. Shah; Ullas V. Chembazhi; Shivjee Sah ; Umesh Varshney
Stoichiometries of U2AF35, U2AF65 and U2 snRNP reveal new early spliceosome assembly pathways border= 
Li Chen; Robert Weinmeister; Jana Kralovicova; Lucy P. Eperon; Igor Vorechovsky ...
A short splicing isoform of HBS1L links the cytoplasmic exosome and SKI complexes in humans border= 
Katarzyna Kalisiak ; Tomasz M. KuliĹ"ski; RafaĹ‚ Tomecki; Dominik Cysewski; Zbigniew Pietras ...
A continuum of mRNP complexes in embryonic microRNA-mediated silencing border= 
Edlyn Wu; Ajay A. Vashisht ; Clément Chapat; Mathieu N. Flamand; Emiliano Cohen ...
Biophysical properties, thermal stability and functional impact of 8-oxo-7,8-dihydroguanine on oligonucleotides of RNA'a study of duplex, hairpins and the aptamer for preQ1 as models border= 
Yu J. Choi; Krzysztof S. Gibala ; Tewoderos Ayele; Katherine V. Deventer; Marino J. E. Resendiz
Molecular determinants for CRISPR RNA maturation in the Cas10'Csm complex and roles for non-Cas nucleases border= 
Forrest C. Walker; Lucy Chou-Zheng; Jack A. Dunkle; Asma Hatoum-Aslan
Identification of 2-methylthio cyclic N6-threonylcarbamoyladenosine (ms2ct6A) as a novel RNA modification at position 37 of tRNAs border= 
Byeong-il Kang; Kenjyo Miyauchi; Michal Matuszewski; Gabriel Silveira D'Almeida; Mary Anne T. Rubio ...
A hydantoin isoform of cyclic N6-threonylcarbamoyladenosine (ct6A) is present in tRNAs border= 
Michal Matuszewski ; Jakub Wojciechowski; Kenjyo Miyauchi; Zofia Gdaniec; Wojciech M. Wolf ...
Structural Biology
Histone chaperone activity of Arabidopsis thaliana NRP1 is blocked by cytochrome c border= 
Katiuska González-Arzola; Antonio DĂ­az-Quintana ; Francisco Rivero-RodrĂ­guez; Adrián Velázquez-Campoy; Miguel A. De la Rosa ...
The AibR-isovaleryl coenzyme A regulator and its DNA binding site ' a model for the regulation of alternative de novo isovaleryl coenzyme A biosynthesis in Myxococcus xanthus  border= 
Tobias Bock; Carsten Volz ; Vanessa Hering; Andrea Scrima; Rolf MĂĽller ...
Structure of a 30S pre-initiation complex stalled by GE81112 reveals structural parallels in bacterial and eukaryotic protein synthesis initiation pathways border=  
Jorge P. LĂłpez-Alonso; Attilio Fabbretti; Tatsuya Kaminishi ; Idoia Iturrioz; Letizia Brandi ...
Interstrand cross-linking implies contrasting structural consequences for DNA: insights from molecular dynamics border= 
Emmanuelle Bignon; Tomáš Dršata; Christophe Morell; Filip Lankaš ; Elise Dumont
Synthetic Biology and Bioengineering
GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data border= 
Marta Vazquez-Vilar; Alfredo Quijano-Rubio; Asun Fernandez-del-Carmen; Alejandro Sarrion-Perdigones; Rocio Ochoa-Fernandez ...
Functionally-interdependent shape-switching nanoparticles with controllable properties border= 
Justin R. Halman ; Emily Satterwhite; Brandon Roark; Morgan Chandler; Mathias Viard ...
A prior-based integrative framework for functional transcriptional regulatory network inference border= 
Alireza F. Siahpirani; Sushmita Roy
Methods Online
A genome-integrated massively parallel reporter assay reveals DNA sequence determinants of cis-regulatory activity in neural cells border= 
Brett B. Maricque; Joseph D. Dougherty; Barak A. Cohen
TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes border= 
Emmanuelle Lerat; Marie Fablet; Laurent Modolo; Hélène Lopez-Maestre ; Cristina Vieira
NOVOPlasty: de novo assembly of organelle genomes from whole genome data border= 
Nicolas Dierckxsens; Patrick Mardulyn; Guillaume Smits
CisMapper: predicting regulatory interactions from transcription factor ChIP-seq data border= 
Timothy O'Connor; Mikael Bodén; Timothy L. Bailey
Using predictive specificity to determine when gene set analysis is biologically meaningful border= 
Sara Ballouz; Paul Pavlidis ; Jesse Gillis
A prior-based integrative framework for functional transcriptional regulatory network inference border= 
Alireza F. Siahpirani; Sushmita Roy
Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes border= 
Wanding Zhou; Peter W. Laird; Hui Shen
Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing border= 
Dieter M. Tourlousse; Satowa Yoshiike ; Akiko Ohashi; Satoko Matsukura; Naohiro Noda ...
A Novel method for the simultaneous identification of methylcytosine and hydroxymethylcytosine at a single base resolution border= 
Yuki Kawasaki; Yukiko Kuroda; Isao Suetake ; Shoji Tajima; Fumitoshi Ishino ...
Discriminative identification of transcriptional responses of promoters and enhancers after stimulus border= 
Dimitrios Kleftogiannis; Panos Kalnis; Erik Arner; Vladimir B. Bajic
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