Subject: Nucleic Acids Research Table of Contents for 7 April 2017 Oxford Academic
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Nucleic Acids Research  
Volume 45 Issue 6
7 April 2017
NAR Breakthrough Article
Molecular mechanism governing ratio-dependent transcription regulation in the ccdAB operon border= 
Alexandra Vandervelde; Igor Drobnak; San Hadži; Yann G.-J. Sterckx ; Thomas Welte ...
Chemical Biology and Nucleic Acid Chemistry
Identification of multiple genomic DNA sequences which form i-motif structures at neutral pH border= 
Elisé P. Wright; Julian L. Huppert; Zoë A. E. Waller
Computational Biology
Bayesian prediction of RNA translation from ribosome profiling border=  
Brandon Malone; Ilian Atanassov; Florian Aeschimann ; Xinping Li; Helge Großhans ...
Knowledge about the presence or absence of miRNA isoforms (isomiRs) can successfully discriminate amongst 32 TCGA cancer types border= 
Aristeidis G. Telonis; Rogan Magee; Phillipe Loher; Inna Chervoneva ; Eric Londin ...
Translational compensation of gene copy number alterations by aneuploidy in Drosophila melanogaster border= 
Zhenguo Zhang; Daven C. Presgraves
Data Resources and Analyses
A critical assessment of topologically associating domain prediction tools border= 
Rola Dali; Mathieu Blanchette
Gene Regulation, Chromatin and Epigenetics
σ38-dependent promoter-proximal pausing by bacterial RNA polymerase border= 
Ivan Petushkov; Daria Esyunina; Andrey Kulbachinskiy
Single-cell profiling reveals that eRNA accumulation at enhancer'promoter loops is not required to sustain transcription border= 
Samir Rahman; Cornelia E. Zorca; Tatiana Traboulsi; Emmanuel Noutahi; Matthew R. Krause ...
Interplay between H1 and HMGN epigenetically regulates OLIG1&2 expression and oligodendrocyte differentiation 
Tao Deng; Yuri Postnikov; Shaofei Zhang; Lillian Garrett ; Lore Becker ...
The CSRP2BP histone acetyltransferase drives smooth muscle gene expression border= 
Yanlin Ma; Qi Li; Ankang Li; Yunjian Wei; Ping Long ...
Nucleosome-free DNA regions differentially affect distant communication in chromatin border= 
Ekaterina V. Nizovtseva; Nicolas Clauvelin ; Stefjord Todolli; Yury S. Polikanov; Olga I. Kulaeva ...
The Drosophila telomere-capping protein Verrocchio binds single-stranded DNA and protects telomeres from DNA damage response border= 
Alessandro Cicconi; Emanuela Micheli; Fiammetta Vernì ; Alison Jackson; Ana Citlali Gradilla ...
H3K27 acetylation activated-long non-coding RNA CCAT1 affects cell proliferation and migration by regulating SPRY4 and HOXB13 expression in esophageal squamous cell carcinoma border= 
Erbao Zhang; Liang Han; Dandan Yin; Xuezhi He ; Linzhi Hong ...
Non-CpG methylation by DNMT3B facilitates REST binding and gene silencing in developing mouse hearts border= 
Donghong Zhang; Bingruo Wu; Ping Wang; Yidong Wang; Pengfei Lu ...
Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression border= 
Rafal Archacki ; Ruslan Yatusevich; Daniel Buszewicz; Katarzyna Krzyczmonik; Jacek Patryn ...
BRD4 promotes p63 and GRHL3 expression downstream of FOXO in mammary epithelial cells border= 
Sankari Nagarajan; Upasana Bedi ; Anusha Budida; Feda H. Hamdan; Vivek Kumar Mishra ...
Genome Integrity, Repair and Replication
Proximity to AGCT sequences dictates MMR-independent versus MMR-dependent mechanisms for AID-induced mutation via UNG2 border= 
Eddy Sanchai Thientosapol; George Sharbeen ; K.K. Edwin Lau; Daniel Bosnjak; Timothy Durack ...
A three-dimensional ParF meshwork assembles through the nucleoid to mediate plasmid segregation border= 
Brett N. McLeod; Gina E. Allison-Gamble; Madhuri T. Barge; Nam K. Tonthat; Maria A. Schumacher ...
DNA-dependent protease activity of human Spartan facilitates replication of DNA'protein crosslink-containing DNA border= 
Mónika Mórocz; Eszter Zsigmond; Róbert Tóth; Márton Zs Enyedi; Lajos Pintér ...
A structure'function analysis of the yeast Elg1 protein reveals the importance of PCNA unloading in genome stability maintenance border= 
Keren Shemesh ; Marek Sebesta; Martin Pacesa; Soumitra Sau; Alex Bronstein ...
Multimerization properties of PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements border= 
Emeline Dubois; Nathalie Mathy ; Vinciane Régnier; Julien Bischerour; Céline Baudry ...
Cdc45-induced loading of human RPA onto single-stranded DNA border= 
Anna Szambowska; Ingrid Tessmer; Piotr Prus; Bernhard Schlott ; Helmut Pospiech ...
Self-cytoplasmic DNA upregulates the mutator enzyme APOBEC3A leading to chromosomal DNA damage border= 
Rodolphe Suspène; Bianka Mussil; Hélène Laude; Vincent Caval; Noémie Berry ...
A novel role for transcription-coupled nucleotide excision repair for the in vivo repair of 3,N4-ethenocytosine border= 
Isaac A. Chaim; Alycia Gardner; Jie Wu; Teruaki Iyama; David M. Wilson, III ...
Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana border= 
Johan Reimegård ; Snehangshu Kundu; Ali Pendle; Vivian F. Irish; Peter Shaw ...
Allele-specific quantitative proteomics unravels molecular mechanisms modulated by cis-regulatory PPARG locus variation border= 
Heekyoung Lee; Kun Qian ; Christine von Toerne; Lena Hoerburger; Melina Claussnitzer ...
Molecular Biology
CNBP acts as a key transcriptional regulator of sustained expression of interleukin-6 border=  
Eunhye Lee; Taeyun A. Lee; Ji Hyun Kim ; Areum Park; Eun A. Ra ...
Spacer-length DNA intermediates are associated with Cas1 in cells undergoing primed CRISPR adaptation border= 
Olga Musharova; Evgeny Klimuk; Kirill A. Datsenko; Anastasia Metlitskaya ; Maria Logacheva ...
Rad6'Bre1-mediated H2B ubiquitination regulates telomere replication by promoting telomere-end resection border= 
Zhenfang Wu; Jun Liu; Qiong-Di Zhang; De-Kang Lv; Nian-Feng Wu ...
The Schizosaccharomyces pombe PPR protein Ppr10 associates with a novel protein Mpa1 and acts as a mitochondrial translational activator border= 
Yirong Wang; Jianhua Yan; Qingzhen Zhang; Xuting Ma; Juan Zhang ...
Nucleic Acid Enzymes
Coordination between the polymerase and RNase H activity of HIV-1 reverse transcriptase border= 
Małgorzata Figiel; Miroslav Krepl ; Jarosław Pozna"ski; Agnieszka Goł.b; Jiří Šponer ...
An in vitro fluorescence based study of initiation of RNA synthesis by influenza B polymerase border= 
Stefan Reich; Delphine Guilligay; Stephen Cusack
DNA editing in DNA/RNA hybrids by adenosine deaminases that act on RNA border= 
Yuxuan Zheng; Claire Lorenzo ; Peter A. Beal
Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization border= 
Madison B. Adolph; Anjuman Ara; Yuqing Feng; Cristina J. Wittkopp; Michael Emerman ...
DNA target recognition domains in the Type I restriction and modification systems of Staphylococcus aureus border= 
Laurie P. Cooper ; Gareth A. Roberts; John H. White; Yvette A. Luyten; Edward K.M. Bower ...
Genetic selection for mistranslation rescues a defective co-chaperone in yeast border= 
Kyle S. Hoffman; Matthew D. Berg ; Brian H. Shilton; Christopher J. Brandl; Patrick O'Donoghue
Spliceosomal protein eftud2 mutation leads to p53-dependent apoptosis in zebrafish neural progenitors border= 
Lei Lei; Shou-Yu Yan; Ran Yang; Jia-Yu Chen ; Yumei Li ...
Poly(A)-specific ribonuclease regulates the processing of small-subunit rRNAs in human cells border= 
Hideaki Ishikawa; Harunori Yoshikawa; Keiichi Izumikawa; Yutaka Miura; Masato Taoka ...
Modulation of nonsense mediated decay by rapamycin border= 
Rocio T. Martinez-Nunez ; Andrew Wallace; Doyle Coyne; Linnea Jansson; Miles Rush ...
The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic border= 
Valérie Cognat; Geoffrey Morelle ; Cyrille Megel; Stéphanie Lalande; Jean Molinier ...
An Ultraconserved Element (UCE) controls homeostatic splicing of ARGLU1 mRNA border= 
Stephan P. Pirnie; Ahmad Osman; Yinzhou Zhu; Gordon G. Carmichael
Application of sorting and next generation sequencing to study 5"-UTR influence on translation efficiency in Escherichia coli border= 
Sergey A. Evfratov; Ilya A. Osterman; Ekaterina S. Komarova; Alexandra M. Pogorelskaya; Maria P. Rubtsova ...
JMJD6 and U2AF65 co-regulate alternative splicing in both JMJD6 enzymatic activity dependent and independent manner border= 
Jia Yi; Hai-Feng Shen ; Jin-Song Qiu; Ming-Feng Huang; Wen-Juan Zhang ...
Functional RNAs: combined assembly and packaging in VLPs border= 
Po-Yu Fang; Lizzette M. Gómez Ramos; Stefany Y. Holguin; Chiaolong Hsiao; Jessica C. Bowman ...
siRNA carrying an (E)-vinylphosphonate moiety at the 5" end of the guide strand augments gene silencing by enhanced binding to human Argonaute-2 border= 
Elad Elkayam; Rubina Parmar; Christopher R. Brown; Jennifer L. Willoughby ; Christopher S. Theile ...
Structural Biology
Structural insights into RNA duplexes with multiple 2"-5"-linkages border= 
Fusheng Shen; Zhipu Luo; Hehua Liu; Rui Wang; Shenglong Zhang ...
Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA border= 
Giedre Tamulaitiene ; Virginija Jovaisaite; Gintautas Tamulaitis; Inga Songailiene; Elena Manakova ...
Nop9 binds the central pseudoknot region of 18S rRNA border= 
Bing Wang; Keqiong Ye
The crystal structure of the 5" functional domain of the transcription riboregulator 7SK border= 
Denise Martinez-Zapien ; Pierre Legrand; Alastair G. McEwen; Florence Proux; Tristan Cragnolini ...
Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism border= 
Rui-Gang Xu; Huw T. Jenkins ; Maria Chechik; Elena V. Blagova; Anna Lopatina ...
The large terminase DNA packaging motor grips DNA with its ATPase domain for cleavage by the flexible nuclease domain border= 
Brendan J. Hilbert; Janelle A. Hayes; Nicholas P. Stone ; Rui-Gang Xu; Brian A. Kelch
Synthetic Biology and Bioengineering
DNA nanostructures constructed with multi-stranded motifs border= 
Donglei Yang; Zhenyu Tan; Yongli Mi; Bryan Wei
Structure and function of human histone H3.Y nucleosome border= 
Tomoya Kujirai; Naoki Horikoshi ; Koichi Sato; Kazumitsu Maehara; Shinichi Machida ...
RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures border= 
Lisanna Paladin; Layla Hirsh; Damiano Piovesan; Miguel A. Andrade-Navarro; Andrey V. Kajava ...
Methods Online
SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing border= 
Amanda Raine; Erika Manlig; Per Wahlberg; Ann-Christine Syvänen; Jessica Nordlund
Identification of novel loci for the generation of reporter mice border= 
Nicoletta Rizzi ; Monica Rebecchi; Giovanna Levandis; Paolo Ciana; Adriana Maggi
Enhanced non-viral gene delivery by coordinated endosomal release and inhibition of beta -tubulin deactylase border= 
Yoon Khei Ho; Li Han Zhou ; Kam C. Tam; Heng Phon Too
Methylation-sensitive enrichment of minor DNA alleles using a double-strand DNA-specific nuclease border= 
Yibin Liu; Chen Song; Ioannis Ladas; Mariana Fitarelli-Kiehl ; G. Mike Makrigiorgos
Cloning-independent markerless gene editing in Streptococcus sanguinis: novel insights in type IV pilus biology border= 
Ishwori Gurung; Jamie-Lee Berry; Alexander M. J. Hall; Vladimir Pelicic
Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes border= 
Zefu Lu; Brigitte T. Hofmeister ; Christopher Vollmers; Rebecca M. DuBois; Robert J. Schmitz
miRTar2GO: a novel rule-based model learning method for cell line specific microRNA target prediction that integrates Ago2 CLIP-Seq and validated microRNA'target interaction data border=  
Alireza Ahadi; Gaurav Sablok; Gyorgy Hutvagner
The combination of direct and paired link graphs can boost repetitive genome assembly border= 
Wenyu Shi; Peifeng Ji ; Fangqing Zhao
QSEA'modelling of genome-wide DNA methylation from sequencing enrichment experiments border= 
Matthias Lienhard; Sabrina Grasse; Jana Rolff; Steffen Frese; Uwe Schirmer ...
A specific DNA-nanoprobe for tracking the activities of human apurinic/apyrimidinic endonuclease 1 in living cells border= 
Junqiu Zhai ; Yibin Liu; Shan Huang; Simin Fang; Meiping Zhao
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