Subject: Nucleic Acids Research Table of Contents for 27 July 2017 Oxford Academic
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Nucleic Acids Research  
Volume 45 Issue 13
27 July 2017
NAR Breakthrough Article
Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome border= 
William C. Hacker; Shuxiang Li; Adrian H. Elcock
Molecular structures guide the engineering of chromatin border= 
Stefan J. Tekel; Karmella A. Haynes
Chemical Biology and Nucleic Acid Chemistry
Determining the folding and binding free energy of DNA-based nanodevices and nanoswitches using urea titration curves border= 
Andrea Idili ; Francesco Ricci; Alexis Vallée-Bélisle
5ő"-Vinylphosphonate improves tissue accumulation and efficacy of conjugated siRNAs in vivo border= 
Reka A. Haraszti; Loic Roux; Andrew H. Coles; Anton A. Turanov ; Julia F. Alterman ...
New insights into a classic aptamer: binding sites, cooperativity and more sensitive adenosine detection border= 
Zijie Zhang; Olatunji Oni; Juewen Liu
Cytosolic delivery of siRNA by ultra-high affinity dsRNA binding proteins border= 
Nicole J. Yang; Monique J. Kauke; Fangdi Sun; Lucy F. Yang ; Katie F. Maass ...
Computational Biology
Family-specific scaling laws in bacterial genomes border= 
Eleonora De Lazzari; Jacopo Grilli; Sergei Maslov; Marco Cosentino Lagomarsino
Crowding-induced transcriptional bursts dictate polymerase and nucleosome density profiles along genes border= 
Aafke A. van den Berg; Martin Depken
Influence of DNA sequence on the structure of minicircles under torsional stress border= 
Qian Wang ; Rossitza N. Irobalieva; Wah Chiu; Michael F. Schmid; Jonathan M. Fogg ...
How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1 border= 
MiŇāosz Wiecz√≥r; Jacek Czub
Gene Regulation, Chromatin and Epigenetics
APOBEC3A efficiently deaminates methylated, but not TET-oxidized, cytosine bases in DNA border= 
Emily K. Schutsky ; Christopher S. Nabel; Amy K. F. Davis; Jamie E. DeNizio; Rahul M. Kohli
Piwi interacts with chromatin at nuclear pores and promiscuously binds nuclear transcripts in Drosophila ovarian somatic cells border= 
Artem A. Ilyin; Sergei S. Ryazansky ; Semen A. Doronin; Oxana M. Olenkina; Elena A. Mikhaleva ...
A c-Myb mutant causes deregulated differentiation due to impaired histone binding and abrogated pioneer factor function border= 
Bettina M. Fuglerud; Roza B. Lemma; Pimthanya Wanichawan ; Arvind Y. M. Sundaram; Ragnhild Eskeland ...
Full shut-off of Escherichia coli RNA-polymerase by T7 phage requires a small phage-encoded DNA-binding protein border= 
Aline Tabib-Salazar; Bing Liu; Andrey Shadrin; Lynn Burchell ; Zhexin Wang ...
The chromatin remodeling complex Swi/Snf regulates splicing of meiotic transcripts in Saccharomyces cerevisiae border= 
Srivats Venkataramanan; Stephen Douglass; Anoop R. Galivanche; Tracy L. Johnson
CHD1 regulates cell fate determination by activation of differentiation-induced genes border= 
Simon J. Baumgart; Zeynab Najafova ; Tareq Hossan; Wanhua Xie; Sankari Nagarajan ...
A viral suppressor of RNA silencing inhibits ARGONAUTE 1 function by precluding target RNA binding to pre-assembled RISC border= 
Erzsébet Kenesi; Alberto Carbonell; Rita Lózsa ; Beáta Vértessy; Lóránt Lakatos
Potential role of DNA methylation as a facilitator of target search processes for transcription factors through interplay with methyl-CpG-binding proteins border= 
Catherine A. Kemme; Rolando Marquez; Ross H. Luu; Junji Iwahara
Genome Integrity, Repair and Replication
Evidence for double-strand break mediated mitochondrial DNA replication in Saccharomyces cerevisiae border= 
Kanchanjunga Prasai ; Lucy C. Robinson; Rona S. Scott; Kelly Tatchell; Lynn Harrison
Crosstalk between vertical and horizontal gene transfer: plasmid replication control by a conjugative relaxase border= 
Fabián Lorenzo-Díaz; Cris Fernández-López; Rudi Lurz; Alicia Bravo; Manuel Espinosa
The interaction between cytosine methylation and processes of DNA replication and repair shape the mutational landscape of cancer genomes border=  
Rebecca C. Poulos; Jake Olivier; Jason W.H. Wong
Mms1 binds to G-rich regions in Saccharomyces cerevisiae and influences replication and genome stability border= 
Katharina Wanzek; Eike Schwindt ; John A. Capra; Katrin Paeschke
Phosphorylated SIRT1 associates with replication origins to prevent excess replication initiation and preserve genomic stability 
Koichi Utani; Haiqing Fu; Sang-Min Jang; Anna B. Marks; Owen K. Smith ...
Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum border= 
Xueqing Maggie Lu ; Gayani Batugedara; Michael Lee; Jacques Prudhomme; Evelien M. Bunnik ...
Genome-wide profiling of S/MAR-based replicon contact sites border= 
Claudia Hagedorn; Andreas Gogol-Döring ; Sabrina Schreiber; Jörg T. Epplen; Hans J. Lipps
Molecular Biology
Interlinked DNA nano-circles for measuring topoisomerase II activity at the level of single decatenation events border= 
Emil L. Kristoffersen; Asger Givskov; Line A. J√łrgensen; Pia W. Jensen; Jo Ann W. Byl ...
Knockdown and replacement therapy mediated by artificial mirtrons in spinocerebellar ataxia 7 border= 
Helen J. Curtis; Yiqi Seow; Matthew J.A. Wood ; Miguel A. Varela
An essential domain of an early-diverged RNA polymerase II functions to accurately decode a primitive chromatin landscape border= 
Anish Das; Mahrukh Banday; Michael A. Fisher; Yun-Juan Chang; Jeffrey Rosenfeld ...
Selective disruption of an oncogenic mutant allele by CRISPR/Cas9 induces efficient tumor regression border= 
Taeyoung Koo ; A-Rum Yoon; Hee-Yeon Cho; Sangsu Bae; Chae-Ok Yun ...
Nucleic Acid Enzymes
T7 RNA polymerase translocation is facilitated by a helix opening on the fingers domain that may also prevent backtracking border= 
Lin-Tai Da; Chao E; Yao Shuai; Shaogui Wu; Xiao-Dong Su ...
A new role for FBP21 as regulator of Brr2 helicase activity border= 
Lisa M. Henning; Karine F. Santos; Jana Sticht; Stefanie Jehle ; Chung-Tien Lee ...
The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts border= 
Birgit Märtens; Linlin Hou; Fabian Amman; Michael T. Wolfinger; Elena Evguenieva-Hackenberg ...
Interplay between miR-574-3p and hnRNP L regulates VEGFA mRNA translation and tumorigenesis border= 
Peng Yao ; Jiangbin Wu; Daniel Lindner; Paul L. Fox
Trypanosome RNA Editing Mediator Complex proteins have distinct functions in gRNA utilization border= 
Rachel M. Simpson; Andrew E. Bruno; Runpu Chen; Kaylen Lott ; Brianna L. Tylec ...
Intrinsically disordered RGG/RG domains mediate degenerate specificity in RNA binding border= 
Bagdeser A. Ozdilek; Valery F. Thompson; Nasiha S. Ahmed; Connor I. White; Robert T. Batey ...
eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs border= 
Daria FijaŇākowska ; Steven Verbruggen; Elvis Ndah; Veronique Jonckheere; Gerben Menschaert ...
Label-free, direct localization and relative quantitation of the RNA nucleobase methylations m6A, m5C, m3U, and m 5U by top-down mass spectrometry border= 
Heidelinde Glasner; Christian Riml ; Ronald Micura; Kathrin Breuker
Major hnRNP proteins act as general TDP-43 functional modifiers both in Drosophila and human neuronal cells border= 
Chiara Appocher; Fatemeh Mohagheghi; Sara Cappelli; Cristiana Stuani ; Maurizio Romano ...
Structural Biology
Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition border= 
Miroslav Krepl; Markus Blatter; Antoine Cléry; Fred F. Damberger; Frédéric H.T. Allain ...
The herpes viral transcription factor ICP4 forms a novel DNA recognition complex border= 
Richard B. Tunnicliffe ; Michael P. Lockhart-Cairns; Colin Levy; A. Paul Mould; Thomas A. Jowitt ...
Molecular envelope and atomic model of an anti-terminated glyQS T-box regulator in complex with tRNAGly  border= 
Bhaskar Chetnani; Alfonso Mondragón
Alternative stable conformation capable of protein misinteraction links tRNA synthetase to peripheral neuropathy border= 
David Blocquel; Sheng Li ; Na Wei; Herwin Daub; Mathew Sajish ...
Synthetic Biology and Bioengineering
The contribution of homology arms to nuclease-assisted genome engineering border=  
Oliver Baker; Sarah Tsurkan; Jun Fu ; Barbara Klink; Andreas Rump ...
Balancing gene expression without library construction via a reusable sRNA pool border= 
Amar Ghodasara; Christopher A. Voigt
Methods Online
Cell-type-specific genome editing with a microRNA-responsive CRISPR'Cas9 switch border= 
Moe Hirosawa; Yoshihiko Fujita; Callum J. C. Parr ; Karin Hayashi; Shunnichi Kashida ...
RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections border= 
Jaime Abraham Castro-Mondragon; S√©bastien Jaeger; Denis Thieffry; Morgane Thomas-Chollier ; Jacques van Helden
ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data border= 
You Li; Tayla B. Heavican; Neetha N. Vellichirammal; Javeed Iqbal; Chittibabu Guda
Identification of active miRNA promoters from nuclear run-on RNA sequencing border= 
Qi Liu ; Jing Wang; Yue Zhao; Chung-I Li; Kristy R. Stengel ...
MiSTIC, an integrated platform for the analysis of heterogeneity in large tumour transcriptome datasets border= 
Sebastien Lemieux; Tobias Sargeant ; David Laperrière; Houssam Ismail; Geneviève Boucher ...
Precise integration of inducible transcriptional elements (PrIITE) enables absolute control of gene expression border= 
Rita Pinto; Lars Hansen; John Hintze; Raquel Almeida; Sylvester Larsen ...
A new computational method to predict transcriptional activity of a DNA sequence from diverse datasets of massively parallel reporter assays border= 
Ying Liu; Takuma Irie; Tetsushi Yada; Yutaka Suzuki
Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules border= 
David Redin; Erik Borgström ; Mengxiao He; Hooman Aghelpasand; Max Käller ...
Statistical algorithms improve accuracy of gene fusion detection border= 
Gillian Hsieh; Rob Bierman; Linda Szabo; Alex Gia Lee ; Donald E. Freeman ...
Gene expression variability and the analysis of large-scale RNA-seq studies with the MDSeq border= 
Di Ran; Z. John Daye
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