Subject: Nucleic Acids Research Table of Contents for 15 December 2017 ------=_Part_1845913752.1513444365530 Content-Type: text/plain;charset=UTF-8 Oxford Academic [[HeaderAdvertisingToken]] https://silverchair.emailcampaigns.net/media/50/509735/OUP/oxford_logo.jpg?g72331686458 (http://click.skem1.com/click/lf6to-d1jujl-66q6ox32/) [[BannerToken]] [[AlertTitleToken]] [[SelfServeTextToken]] [[FirstAdvertisingToken]] [[TOCMainToken]] Unsubscribe (http://click.skem1.com/form?lf6to--ply5-66q6ox35&sl=tq&t=5)Manage email alerts (http://click.skem1.com/click/lf6to-d1jujm-66q6ox33/) 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. https://silverchair.emailcampaigns.net/media/50/509735/OUP/oxforde_university.jpg?g72331733632 (http://click.skem1.com/click/lf6to-d1jujn-66q6ox34/) [[BottomAdvertisingToken]] This email is intended for bionet@evol.mcmaster.ca. ------=_Part_1845913752.1513444365530 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Nucleic Acids Research  
Volume 45 Issue 22
 
15 December 2017
 
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NAR Breakthrough Article
 
 
 
Logical engineering of D-arm and T-stem of tRNA that enhances d-amino acid incorporation border= 
 
Takayuki Katoh; Yoshihiko Iwane; Hiroaki Suga
 
 
SURVEY AND SUMMARY
 
 
 
Conserved non-coding elements: developmental gene regulation meets genome organization border= 
 
Dimitris Polychronopoulos; James W. D. King; Alexander J. Nash; Ge Tan; Boris Lenhard
 
 
Meta-analysis of DNA double-strand break response kinetics border= 
 
Jakub A. Kochan; Emilie C.B. Desclos; Ruben Bosch; Luna Meister ; Lianne E.M. Vriend ...
 
 
Computational Biology
 
 
 
Structure modeling of RNA using sparse NMR constraints border= 
 
Benfeard Williams, II; Bo Zhao; Arpit Tandon; Feng Ding; Kevin M. Weeks ...
 
 
Insilico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level border= 
 
Changwon Yang ; Mandar Kulkarni; Manho Lim; Youngshang Pak
 
 
 
 
Data Resources and Analyses
 
 
 
Discovering cancer vulnerabilities using high-throughput micro-RNA screening border= 
 
Iva Nikolic; Benjamin Elsworth; Eoin Dodson ; Sunny Z. Wu; Cathryn M. Gould ...
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
The mechanism and high-free-energy transition state of lac repressor'lac operator interaction border= 
 
Rituparna Sengupta; Michael W. Capp; Irina A. Shkel; M. Thomas Record, Jr
 
 
Epigenetic mechanisms underlie the crosstalk between growth factors and a steroid hormone border= 
 
Yehoshua Enuka ; Morris E. Feldman; Animesh Chowdhury; Swati Srivastava; Moshit Lindzen ...
 
 
Tet1 facilitates hypoxia tolerance by stabilizing the HIF-alpha proteins independent of its methylcytosine dioxygenase activity border= 
 
Jing Wang; Dawei Zhang; Juan Du; Chi Zhou; Zhi Li ...
 
 
Global inhibition of transcription causes an increase in histone H2A.Z incorporation within gene bodies border= 
 
Anahita Lashgari; Jean-François Millau; Pierre-Étienne Jacques ; Luc Gaudreau
 
 
 
 
Rif1 promotes a repressive chromatin state to safeguard against endogenous retrovirus activation 
 
Pishun Li; Li Wang ; Brian D. Bennett; Jiajia Wang; Jialun Li ...
 
 
Characteristic arrangement of nucleosomes is predictive of chromatin interactions at kilobase resolution border= 
 
Hui Zhang; Feifei Li; Yan Jia; Bingxiang Xu ; Yiqun Zhang ...
 
 
Accumulation of long-term transcriptionally active integrated retroviral vectors in active promoters and enhancers border= 
 
Filip Ċ enigl; Dalibor Miklík; Miroslav Auxt; JiĊ™í Hejnar
 
 
Loss of imprinting mutations define both distinct and overlapping roles for misexpression of IGF2 and of H19 lncRNA  
 
Ki-Sun Park; Apratim Mitra; Beenish Rahat ; Keekwang Kim; Karl Pfeifer
 
 
Independence between pre-mRNA splicing and DNA methylation in an isogenic minigene resource 
 
Kyster K. Nanan; Cody Ocheltree; David Sturgill; Mariana D. Mandler; Maria Prigge ...
 
 
CsrA maximizes expression of the AcrAB multidrug resistance transporter border= 
 
Vito Ricci ; Victoria Attah; Tim Overton; David C. Grainger; Laura J.V. Piddock
 
 
Genome Integrity, Repair and Replication
 
 
 
Aberrant ribonucleotide incorporation and multiple deletions in mitochondrial DNA of the murine MPV17 disease model border= 
 
Chloe F. Moss; Ilaria Dalla Rosa; Lilian E. Hunt; Takehiro Yasukawa; Robert Young ...
 
 
The RNA processing factors THRAP3 and BCLAF1 promote the DNA damage response through selective mRNA splicing and nuclear export border=  
 
Jekaterina Vohhodina; Eliana M. Barros; Abigail L. Savage ; Fabio G. Liberante; Lorenzo Manti ...
 
 
PARP1 changes from three-dimensional DNA damage searching to one-dimensional diffusion after auto-PARylation or in the presence of APE1 border= 
 
Lili Liu; Muwen Kong; Natalie R. Gassman; Bret D. Freudenthal ; Rajendra Prasad ...
 
 
Secondary structure forming sequences drive SD-MMEJ repair of DNA double-strand breaks border= 
 
Varandt Y. Khodaverdian; Terrence Hanscom; Amy Marie Yu; Taylor L. Yu; Victoria Mak ...
 
 
RBM45 competes with HDAC1 for binding to FUS in response to DNA damage border= 
 
Juanjuan Gong ; Min Huang; Fengli Wang; Xiaolu Ma; Hongmei Liu ...
 
 
Genomics
 
 
 
Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding border= 
 
Jinsen Li; Jared M. Sagendorf ; Tsu-Pei Chiu; Marco Pasi; Alberto Perez ...
 
 
Molecular Biology
 
 
 
Discovering the 3² UTR-mediated regulation of alpha-synuclein border=  
 
Domenica Marchese; Teresa Botta-Orfila; Davide Cirillo ; Juan Antonio Rodriguez; Carmen Maria Livi ...
 
 
NS3 helicase from dengue virus specifically recognizes viral RNA sequence to ensure optimal replication border= 
 
Crystall M. D. Swarbrick; Chandrakala Basavannacharya; Kitti W. K. Chan; Shu-Ann Chan ; Daljit Singh ...
 
 
Derivation of nearest-neighbor DNA parameters in magnesium from single molecule experiments border= 
 
Josep Maria Huguet; Marco Ribezzi-Crivellari; Cristiano Valim Bizarro; Felix Ritort
 
 
Nucleic Acid Enzymes
 
 
 
RNase H sequence preferences influence antisense oligonucleotide efficiency border= 
 
Ċ ukasz J. KieĊ‚piĊ"ski; Peter H. Hagedorn ; Morten Lindow; Jeppe Vinther
 
 
Structural basis for the GTP specificity of the RNA kinase domain of fungal tRNA ligase border= 
 
Barbara S. Remus; Yehuda Goldgur; Stewart Shuman
 
 
The mechano-chemistry of a monomeric reverse transcriptase border= 
 
Omri Malik; Hadeel Khamis ; Sergei Rudnizky; Ariel Kaplan
 
 
RNA and RNA-protein complexes
 
 
 
Polycytidylation of mitochondrial mRNAs in Chlamydomonas reinhardtii border= 
 
Thalia Salinas-Giegé; Marina Cavaiuolo; Valérie Cognat; Elodie Ubrig ; Claire Remacle ...
 
 
Biogenesis and iron-dependency of ribosomal RNA hydroxylation border= 
 
Satoshi Kimura; Yusuke Sakai; Kensuke Ishiguro; Tsutomu Suzuki
 
 
Conserved structures formed by heterogeneous RNA sequences drive silencing of an inflammation responsive post-transcriptional operon border= 
 
Abhijit Basu ; Niyati Jain; Blanton S. Tolbert; Anton A. Komar; Barsanjit Mazumder
 
 
Multiple RNA structures affect translation initiation and UGA redefinition efficiency during synthesis of selenoprotein P border= 
 
Marco Mariotti; Sumangala Shetty; Lisa Baird; Sen Wu; Gary Loughran ...
 
 
Distinct roles for the IIId2 sub-domain in pestivirus and picornavirus internal ribosome entry sites border= 
 
Margaret M. Willcocks; Salmah Zaini; Nathalie Chamond; Nathalie Ulryck; Delphine Allouche ...
 
 
Structural Biology
 
 
 
Structure of the large terminase from a hyperthermophilic virus reveals a unique mechanism for oligomerization and ATP hydrolysis border= 
 
Rui-Gang Xu; Huw T. Jenkins; Alfred A. Antson; Sandra J. Greive
 
 
Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways border= 
 
Masahiko Okuda; Yuka Nakazawa ; Chaowan Guo; Tomoo Ogi; Yoshifumi Nishimura
 
 
Conformational profiling of a G-rich sequence within the c-KIT promoter border= 
 
Riccardo Rigo; William L. Dean; Robert D. Gray; Jonathan B. Chaires ; Claudia Sissi
 
 
Structural basis for the functional role of the Shu complex in homologous recombination border= 
 
Shicheng Zhang; Linlin Wang; Ye Tao; Tuya Bai; Rong Lu ...
 
 
Structural basis of effector and operator recognition by the phenolic acid-responsive transcriptional regulator PadR border= 
 
Sun Cheol Park ; Yun Mi Kwak; Wan Seok Song; Minsun Hong; Sung-il Yoon
 
 
Corrigendum
 
 
 
Phospho-epitope binding by the BRCT domains of hPTIP controls multiple aspects of the cellular response to DNA damage border= 
 
Ivan M. Munoz; Paul A. Jowsey; Rachel Toth; John Rouse
 
 
Identification of multiple genomic DNA sequences which form i-motif structures at neutral pH border= 
 
Elisé P. Wright; Julian L. Huppert; Zöe A.E. Waller
 
 
Linnorm: improved statistical analysis for single cell RNA-seq expression data border= 
 
Shun H. Yip; Panwen Wang ; Jean-Pierre A. Kocher; Pak Chung Sham; Junwen Wang
 
 
Methods Online
 
 
 
Linnorm: improved statistical analysis for single cell RNA-seq expression data border=  
 
Shun H. Yip; Panwen Wang; Jean-Pierre A. Kocher ; Pak Chung Sham; Junwen Wang
 
 
Arrayed mutant haploid embryonic stem cell libraries facilitate phenotype-driven genetic screens border= 
 
Guang Liu; Xue Wang; Yufang Liu; Meili Zhang ; Tao Cai ...
 
 
Design and implementation of a synthetic pre-miR switch for controlling miRNA biogenesis in mammals border= 
 
Janina Atanasov; Florian Groher; Julia E. Weigand; Beatrix Suess
 
 
Optimizing DNA assembly based on statistical language modelling border= 
 
Gang Fang; Shemin Zhang ; Yafei Dong
 
 
PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea border= 
 
Urminder Singh; Niraj Khemka; Mohan Singh Rajkumar; Rohini Garg; Mukesh Jain
 
 
Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C border= 
 
A. Marieke Oudelaar ; James O.J. Davies; Damien J. Downes; Douglas R. Higgs; Jim R. Hughes
 
 
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