Subject: Nucleic Acids Research Table of Contents for 20 April 2017 Oxford Academic
 
 
 
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New issue alert
 
Nucleic Acids Research  
Volume 45 Issue 7
 
20 April 2017
 
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NAR Breakthrough Article
 
 
 
Measurements of translation initiation from all 64 codons in E. coli 
 
Ariel Hecht; Jeff Glasgow; Paul R. Jaschke; Lukmaan A. Bawazer; Matthew S. Munson ...
 
 
SURVEY AND SUMMARY
 
 
 
Use it or lose it: citations predict the continued online availability of published bioinformatics resources border= 
 
Jonathan D. Wren ; Constantin Georgescu; Cory B. Giles; Jason Hennessey
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Iron mediates catalysis of nucleic acid processing enzymes: support for Fe(II) as a cofactor before the great oxidation event border= 
 
C. Denise Okafor; Kathryn A. Lanier; Anton S. Petrov; Shreyas S. Athavale; Jessica C. Bowman ...
 
 
Computational Biology
 
 
 
Consecutive non-natural PZ nucleobase pairs in DNA impact helical structure as seen in 50 mu s molecular dynamics simulations border= 
 
Robert W. Molt, Jr; Millie M. Georgiadis; Nigel G.J. Richards
 
 
Conformational polymorphism or structural invariance in DNA photoinduced lesions: implications for repair rates border= 
 
François Dehez; Hugo Gattuso; Emmanuelle Bignon; Christophe Morell; Elise Dumont ...
 
 
 
 
Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings border= 
 
Natalie Sauerwald; She Zhang; Carl Kingsford; Ivet Bahar
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
KDM4B/JMJD2B is a p53 target gene that modulates the amplitude of p53 response after DNA damage border= 
 
Laura Castellini; Eui Jung Moon; Olga V. Razorenova; Adam J. Krieg ; Rie von Eyben ...
 
 
Inducible super-enhancers are organized based on canonical signal-specific transcription factor binding elements border= 
 
Dóra Bojcsuk; Gergely Nagy; Balint L. Balint
 
 
Efficient DNA binding of NF-kappa B requires the chaperone-like function of NPM1 border= 
 
Jianhuang Lin; Mitsuyasu Kato; Kyosuke Nagata; Mitsuru Okuwaki
 
 
The replication initiator of the cholera pathogen's second chromosome shows structural similarity to plasmid initiators border= 
 
Natalia Orlova ; Matthew Gerding; Olha Ivashkiv; Paul Dominic B. Olinares; Brian T. Chait ...
 
 
 
 
Positive feedback loop mediated by protein phosphatase 1alpha mobilization of P-TEFb and basal CDK1 drives androgen receptor in prostate cancer border=  
 
Xiaming Liu; Yanfei Gao; HuiHui Ye ; Sean Gerrin; Fen Ma ...
 
 
INO80 represses osmostress induced gene expression by resetting promoter proximal nucleosomes border= 
 
Eva Klopf; Heiko A. Schmidt; Sandra Clauder-Münster; Lars M. Steinmetz ; Christoph Schüller
 
 
PHF1 Tudor and N-terminal domains synergistically target partially unwrapped nucleosomes to increase DNA accessibility border= 
 
Matthew D. Gibson; Jovylyn Gatchalian; Andrew Slater; Tatiana G. Kutateladze; Michael G. Poirier
 
 
Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies border= 
 
Nicolae Radu Zabet ; Marco Catoni; Filippo Prischi; Jerzy Paszkowski
 
 
A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea border= 
 
Irina A. Rodionova; Matthew W. Vetting; Xiaoqing Li; Steven C. Almo ; Andrei L. Osterman ...
 
 
The histone demethylase PHF8 is a molecular safeguard of the IFNgamma response border= 
 
Elena Asensio-Juan; Raquel Fueyo; Stella Pappa; Simona Iacobucci; Carmen Badosa ...
 
 
Genome Integrity, Repair and Replication
 
 
 
Deletion of the rnl gene encoding a nick-sealing RNA ligase sensitizes Deinococcus radiodurans to ionizing radiation border= 
 
Brad J. Schmier; Xinguo Chen; Sandra Wolin; Stewart Shuman
 
 
DNA polymerase beta uses its lyase domain in a processive search for DNA damage 
 
Michael J. Howard; Yesenia Rodriguez; Samuel H. Wilson
 
 
Recognition but no repair of abasic site in single-stranded DNA by human ribosomal uS3 protein residing within intact 40S subunit border= 
 
Anastasia S. Grosheva ; Dmitry O. Zharkov; Joachim Stahl; Alexander V. Gopanenko; Alexey E. Tupikin ...
 
 
WRN is recruited to damaged telomeres via its RQC domain and tankyrase1-mediated poly-ADP-ribosylation of TRF1 border= 
 
Luxi Sun; Satoshi Nakajima ; Yaqun Teng; Hao Chen; Lu Yang ...
 
 
Regulation of telomere metabolism by the RNA processing protein Xrn1 border= 
 
Daniele Cesena; Corinne Cassani; Emanuela Rizzo; Michael Lisby ; Diego Bonetti ...
 
 
The structure and function of an RNA polymerase interaction domain in the PcrA/UvrD helicase border= 
 
Kelly Sanders; Chia-Liang Lin; Abigail J. Smith; Nora Cronin; Gemma Fisher ...
 
 
Dynamic assembly of Hda and the sliding clamp in the regulation of replication licensing border= 
 
Jin S. Kim ; Michael T. Nanfara; Sundari Chodavarapu; Kyeong S. Jin; Vignesh M. P. Babu ...
 
 
Tankyrase1-mediated poly(ADP-ribosyl)ation of TRF1 maintains cell survival after telomeric DNA damage border= 
 
Lu Yang; Luxi Sun ; Yaqun Teng; Hao Chen; Ying Gao ...
 
 
Genomics
 
 
 
Comparative genomic analysis of translation initiation mechanisms for genes lacking the Shine'Dalgarno sequence in prokaryotes border= 
 
So Nakagawa; Yoshihito Niimura; Takashi Gojobori
 
 
Molecular Biology
 
 
 
The impact of base stacking on the conformations and electrostatics of single-stranded DNA border= 
 
Alex Plumridge; Steve P. Meisburger; Kurt Andresen; Lois Pollack
 
 
Antibiotics trigger initiation of SCCmec transfer by inducing SOS responses border= 
 
Pilong Liu; Zhaowei Wu ; Huping Xue; Xin Zhao
 
 
Handcuffing reversal is facilitated by proteases and replication initiator monomers border= 
 
Katarzyna Bury; Katarzyna Wegrzyn; Igor Konieczny
 
 
Nucleic Acid Enzymes
 
 
 
Arm-specific cleavage and mutation during reverse transcription of 2Î",5Î"-branched RNA by Moloney murine leukemia virus reverse transcriptase border= 
 
Jessica Döring ; Thomas Hurek
 
 
Editing of misaminoacylated tRNA controls the sensitivity of amino acid stress responses in Saccharomyces cerevisiae border= 
 
Kyle Mohler; Rebecca Mann; Tammy J. Bullwinkle; Kyle Hopkins; Lin Hwang ...
 
 
A thermostable d-polymerase for mirror-image PCR border= 
 
Andreas Pech ; John Achenbach; Michael Jahnz; Simone Schülzchen; Florian Jarosch ...
 
 
RNA
 
 
 
The 5Î" UTR of the type I toxin ZorO can both inhibit and enhance translation border= 
 
Jia Wen; John R. Harp ; Elizabeth M. Fozo
 
 
Identification of senescence-associated circular RNAs (SAC-RNAs) reveals senescence suppressor CircPVT1 
 
Amaresh C. Panda ; Ioannis Grammatikakis; Kyoung Mi Kim; Supriyo De; Jennifer L. Martindale ...
 
 
The influence of the 5Î"-terminal nucleotide on AgoshRNA activity and biogenesis: importance of the polymerase III transcription initiation site border= 
 
Elena Herrera-Carrillo ; Zong-liang Gao; Alex Harwig; Matthias T. Heemskerk; Ben Berkhout
 
 
Modulation of the splicing regulatory function of SRSF10 by a novel compound that impairs HIV-1 replication border= 
 
Lulzim Shkreta; Marco Blanchette ; Johanne Toutant; Emmanuelle Wilhelm; Brendan Bell ...
 
 
Regulation of Prp43-mediated disassembly of spliceosomes by its cofactors Ntr1 and Ntr2 border= 
 
Jean-Baptiste Fourmann; Marcel J. Tauchert; Ralf Ficner; Patrizia Fabrizio; Reinhard Lührmann
 
 
A genetically encoded fluorescent tRNA is active in live-cell protein synthesis border= 
 
Isao Masuda; Takao Igarashi; Reiko Sakaguchi; Ram G. Nitharwal; Ryuichi Takase ...
 
 
The RNA-binding protein Secisbp2 differentially modulates UGA codon reassignment and RNA decay border= 
 
Noelia Fradejas-Villar ; Sandra Seeher; Christine B. Anderson; Michael Doengi; Bradley A. Carlson ...
 
 
Applicability of a computational design approach for synthetic riboswitches border= 
 
Gesine Domin; Sven Findeiß ; Manja Wachsmuth; Sebastian Will; Peter F. Stadler ...
 
 
Binding site density enables paralog-specific activity of SLM2 and Sam68 proteins in Neurexin2 AS4 splicing control border= 
 
Marina Danilenko; Caroline Dalgliesh; Vittoria Pagliarini ; Chiara Naro; Ingrid Ehrmann ...
 
 
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 ...
 
 
MicroRNA-202 maintains spermatogonial stem cells by inhibiting cell cycle regulators and RNA binding proteins border= 
 
Jian Chen; Tanxi Cai; Chunwei Zheng; Xiwen Lin; Guojun Wang ...
 
 
Argonaute proteins regulate HIV-1 multiply spliced RNA and viral production in a Dicer independent manner border= 
 
Agathe Eckenfelder ; Emmanuel Ségéral; Natalia Pinzón; Damien Ulveling; Céline Amadori ...
 
 
Expression of the eRF1 translation termination factor is controlled by an autoregulatory circuit involving readthrough and nonsense-mediated decay in plants border= 
 
Tünde Nyikó ; Andor Auber; Levente Szabadkai; Anna Benkovics; Mariann Auth ...
 
 
ADAR2 regulates RNA stability by modifying access of decay-promoting RNA-binding proteins border= 
 
Aparna Anantharaman; Vidisha Tripathi ; Abid Khan; Je-Hyun Yoon; Deepak K. Singh ...
 
 
Succession of splicing regulatory elements determines cryptic 5Î"ss functionality border= 
 
Anna-Lena Brillen; Katrin Schöneweis; Lara Walotka; Linda Hartmann ; Lisa Müller ...
 
 
Structural Biology
 
 
 
How accurate are accurate force-fields for B-DNA? border= 
 
Pablo D. Dans; Ivan Ivani; Adam Hospital; Guillem Portella; Carlos González ...
 
 
Insights into the RecQ helicase mechanism revealed by the structure of the helicase domain of human RECQL5 border= 
 
Joseph A. Newman ; Hazel Aitkenhead; Pavel Savitsky; Opher Gileadi
 
 
Structural basis of operator sites recognition and effector binding in the TetR family transcription regulator FadR border= 
 
Hyun Ku Yeo; Young Woo Park; Jae Young Lee
 
 
RNA binding and chaperone activity of the E. coli cold-shock protein CspA border= 
 
Enrico Rennella; Tomáš Sára ; Michael Juen; Christoph Wunderlich; Lionel Imbert ...
 
 
Analyzing DNA curvature and its impact on the ionic environment: application to molecular dynamics simulations of minicircles border= 
 
Marco Pasi; Krystyna Zakrzewska; John H. Maddocks ; Richard Lavery
 
 
Erratum
 
 
 
JET2 Viewer: a database of predicted multiple, possibly overlapping, protein'protein interaction sites for PDB structures border= 
 
Hugues Ripoche; Elodie Laine; Nicoletta Ceres; Alessandra Carbone
 
 
Updates in Rhea ' an expert curated resource of biochemical reactions border= 
 
Anne Morgat; Thierry Lombardot ; Kristian B. Axelsen; Lucila Aimo; Anne Niknejad ...
 
 
Methods Online
 
 
 
Query-seeded iterative sequence similarity searching improves selectivity 5'20-fold border=  
 
William R. Pearson; Weizhong Li; Rodrigo Lopez
 
 
Physico-chemical fingerprinting of RNA genes border= 
 
Ankita Singh; Akhilesh Mishra ; Ali Khosravi; Garima Khandelwal; B. Jayaram
 
 
A cost effective 5Î" selective single cell transcriptome profiling approach with improved UMI design border= 
 
Marie-Jeanne Arguel; Kevin LeBrigand; Agnès Paquet; Sandra Ruiz García; Laure-Emmanuelle Zaragosi ...
 
 
Efficient size-independent chromosome delivery from yeast to cultured cell lines border= 
 
David M. Brown; Yujia A. Chan; Prashant J. Desai; Peter Grzesik; Lauren M. Oldfield ...
 
 
miSTAR: miRNA target prediction through modeling quantitative and qualitative miRNA binding site information in a stacked model structure border= 
 
Gert Van Peer; Ayla De Paepe; Michiel Stock; Jasper Anckaert; Pieter-Jan Volders ...
 
 
pBACode: a random-barcode-based high-throughput approach for BAC paired-end sequencing and physical clone mapping border= 
 
Xiaolin Wei; Zhichao Xu ; Guixing Wang; Jilun Hou; Xiaopeng Ma ...
 
 
Flexible model-based clustering of mixed binary and continuous data: application to genetic regulation and cancer border= 
 
Fatin N. Zainul Abidin; David R. Westhead
 
 
SLICE: determining cell differentiation and lineage based on single cell entropy border= 
 
Minzhe Guo; Erik L. Bao ; Michael Wagner; Jeffrey A. Whitsett; Yan Xu
 
 
An optimized, broadly applicable piggyBac transposon induction system border= 
 
Zongtai Qi; Michael Nathaniel Wilkinson; Xuhua Chen; Sumithra Sankararaman; David Mayhew ...
 
 
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