Subject: Nucleic Acids Research Table of Contents for 5 May 2017 Oxford Academic
 
 
 
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New issue alert
 
Nucleic Acids Research  
Volume 45 Issue 8
 
5 May 2017
 
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NAR Breakthrough Article
 
 
 
CTC1-mediated C-strand fill-in is an essential step in telomere length maintenance border= 
 
Xuyang Feng; Shih-Jui Hsu; Christopher Kasbek; Mary Chaiken ; Carolyn M. Price
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Clustered abasic lesions profoundly change the structure and stability of human telomeric G-quadruplexes border= 
 
Iva Kejnovská; Klára Bednářová; Daniel Renčiuk; Zuzana Dvořáková; Petra Školáková ...
 
 
Programmable i-motif DNA folding topology for a pH-switched reversible molecular sensing device border= 
 
Lili Shi ; Pai Peng; Yi Du; Tao Li
 
 
Computational Biology
 
 
 
Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility border= 
 
Xi Chen; Bowen Yu; Nicholas Carriero ; Claudio Silva; Richard Bonneau
 
 
Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence border= 
 
Alon Diament; Tamir Tuller
 
 
 
 
Data Resources and Analyses
 
 
 
Dynamically and epigenetically coordinated GATA/ETS/SOX transcription factor expression is indispensable for endothelial cell differentiation border=  
 
Yasuharu Kanki; Ryo Nakaki; Teppei Shimamura ; Taichi Matsunaga; Kohei Yamamizu ...
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
PRMT5 regulates IRES-dependent translation via methylation of hnRNP A1 border= 
 
Guozhen Gao; Surbhi Dhar; Mark T Bedford
 
 
The novel lysine specific methyltransferase METTL21B affects mRNA translation through inducible and dynamic methylation of Lys-165 in human eukaryotic elongation factor 1 alpha (eEF1A) border= 
 
Jędrzej Małecki ; Vinay Kumar Aileni; Angela Y.Y. Ho; Juliane Schwarz; Anders Moen ...
 
 
Body-hypomethylated human genes harbor extensive intragenic transcriptional activity and are prone to cancer-associated dysregulation border= 
 
Isabel Mendizabal ; Jia Zeng; Thomas E. Keller; Soojin V. Yi
 
 
Sustained expression of miR-26a promotes chromosomal instability and tumorigenesis through regulation of CHFR border= 
 
Leandro Castellano; Aleksandra Dabrowska; Loredana Pellegrino ; Silvia Ottaviani; Paul Cathcart ...
 
 
 
 
Sas3 and Ada2(Gcn5)-dependent histone H3 acetylation is required for transcription elongation at the de-repressed FLO1 gene border= 
 
Michael Church; Kim C. Smith; Mohamed M. Alhussain; Sari Pennings; Alastair B. Fleming
 
 
Wide-ranging and unexpected consequences of altered Pol II catalytic activity in vivo border= 
 
Indranil Malik ; Chenxi Qiu; Thomas Snavely; Craig D. Kaplan
 
 
Interaction with ZMYND11 mediates opposing roles of Ras-responsive transcription factors ETS1 and ETS2 border= 
 
Joshua P. Plotnik; Peter C. Hollenhorst
 
 
Deciphering the DNA code for the function of the Drosophila polydactyl zinc finger protein Suppressor of Hairy-wing border=  
 
Ryan M. Baxley; James D. Bullard; Michael W. Klein ; Ashley G. Fell; Joel A. Morales-Rosado ...
 
 
Long non-coding RNAs transcribed by ERV-9 LTR retrotransposon act in cis to modulate long-range LTR enhancer function border= 
 
Tianxiang Hu; Wenhu Pi; Xingguo Zhu; Miao Yu ; Hongseok Ha ...
 
 
Abf1 and other general regulatory factors control ribosome biogenesis gene expression in budding yeast border= 
 
Maria Cristina Bosio; Beatrice Fermi; Gloria Spagnoli; Elisabetta Levati; Ludmilla Rubbi ...
 
 
Genome Integrity, Repair and Replication
 
 
 
Architectural plasticity of human BRCA2'RAD51 complexes in DNA break repair border= 
 
Humberto Sánchez ; Maarten W. Paul; Małgorzata Grosbart; Sarah E. van Rossum-Fikkert; Joyce H. G. Lebbink ...
 
 
Differential requirement of Srs2 helicase and Rad51 displacement activities in replication of hairpin-forming CAG/CTG repeats border= 
 
Jennifer H.G. Nguyen ; David Viterbo; Ranjith P. Anand; Lauren Verra; Laura Sloan ...
 
 
Ataxin-3 promotes genome integrity by stabilizing Chk1 border= 
 
Yingfeng Tu; Hongmei Liu ; Xuefei Zhu; Hongyan Shen; Xiaolu Ma ...
 
 
Human CTF18-RFC clamp-loader complexed with non-synthesising DNA polymerase epsilon efficiently loads the PCNA sliding clamp border= 
 
Ryo Fujisawa; Eiji Ohashi; Kouji Hirota; Toshiki Tsurimoto
 
 
Spartan deficiency causes accumulation of Topoisomerase 1 cleavage complexes and tumorigenesis border= 
 
Reeja S. Maskey ; Karen S. Flatten; Cynthia J. Sieben; Kevin L. Peterson; Darren J. Baker ...
 
 
Repair of UV-induced DNA lesions in natural Saccharomyces cerevisiae telomeres is moderated by Sir2 and Sir3, and inhibited by yKu'Sir4 interaction border= 
 
Laetitia Guintini; Maxime Tremblay ; Martin Toussaint; Annie D'Amours; Ralf E. Wellinger ...
 
 
RAD51 interconnects between DNA replication, DNA repair and immunity border= 
 
Souparno Bhattacharya; Kalayarasan Srinivasan; Salim Abdisalaam; Fengtao Su; Prithvi Raj ...
 
 
Genomics
 
 
 
Functional assessment of CTCF sites at cytokine-sensing mammary enhancers using CRISPR/Cas9 gene editing in mice 
 
Hye Kyung Lee ; Michaela Willi; Chaochen Wang; Chul Min Yang; Harold E. Smith ...
 
 
Molecular Biology
 
 
 
Aicardi'Goutières syndrome protein TREX1 suppresses L1 and maintains genome integrity through exonuclease-independent ORF1p depletion border= 
 
Peng Li; Juan Du; John L. Goodier; Jingwei Hou; Jian Kang ...
 
 
A DEAD-box protein acts through RNA to promote HIV-1 Rev-RRE assembly border= 
 
Rajan Lamichhane; John A. Hammond; Raymond F. Pauszek, III; Rae M. Anderson; Ingemar Pedron ...
 
 
The spacer size of I-B CRISPR is modulated by the terminal sequence of the protospacer border= 
 
Ming Li; Luyao Gong; Dahe Zhao; Jian Zhou; Hua Xiang
 
 
Nucleic Acid Enzymes
 
 
 
Inhibition of homologous phosphorolytic ribonucleases by citrate may represent an evolutionarily conserved communicative link between RNA degradation and central metabolism border= 
 
Carlanne M. Stone; Louise E. Butt; Joshua C. Bufton; Daniel C. Lourenco; Darren M. Gowers ...
 
 
In vivo cleavage specificity of Trypanosoma brucei editosome endonucleases border= 
 
Jason Carnes ; Suzanne McDermott; Atashi Anupama; Brian G. Oliver; D. Noah Sather ...
 
 
Annealing helicase HARP closes RPA-stabilized DNA bubbles non-processively border= 
 
Daniel R. Burnham; Bas Nijholt ; Iwijn De Vlaminck; Jinhua Quan; Timur Yusufzai ...
 
 
NAP1L1 accelerates activation and decreases pausing to enhance nucleosome remodeling by CSB border= 
 
Ju Yeon Lee; Robert J. Lake; Jaewon Kirk; Vilhelm A. Bohr ; Hua-Ying Fan ...
 
 
RNA
 
 
 
The RNA ligase RtcB reverses MazF-induced ribosome heterogeneity in Escherichia coli border= 
 
Hannes Temmel; Christian Müller; Martina Sauert; Oliver Vesper; Ariela Reiss ...
 
 
A meiosis-specific Spt5 homolog involved in non-coding transcription border= 
 
Julita Gruchota ; Cyril Denby Wilkes; Olivier Arnaiz; Linda Sperling; Jacek K. Nowak
 
 
Divalent ion competition reveals reorganization of an RNA ion atmosphere upon folding border= 
 
Robert J. Trachman, III; David E. Draper
 
 
Differential hepatitis C virus RNA target site selection and host factor activities of naturally occurring miR-122 3" variants border= 
 
Daisuke Yamane ; Sara R. Selitsky; Tetsuro Shimakami; You Li; Mi Zhou ...
 
 
KSHV SOX mediated host shutoff: the molecular mechanism underlying mRNA transcript processing border= 
 
Hyunah Lee; Anathe O.M. Patschull ; Claire Bagnéris; Hannah Ryan; Christopher M. Sanderson ...
 
 
Short intron-derived ncRNAs border= 
 
Florent Hubé; Damien Ulveling; Alain Sureau; Sabrina Forveille ; Claire Francastel
 
 
Mechanistic insights into type I toxin antitoxin systems in Helicobacter pylori: the importance of mRNA folding in controlling toxin expression border= 
 
Hélène Arnion; Dursun Nizam Korkut; Sara Masachis Gelo; Sandrine Chabas; Jérémy Reignier ...
 
 
The ribosome biogenesis factor yUtp23/hUTP23 coordinates key interactions in the yeast and human pre-40S particle and hUTP23 contains an essential PIN domain border= 
 
Graeme R. Wells; Franziska Weichmann; Katherine E. Sloan; David Colvin; Nicholas J. Watkins ...
 
 
microRNAs stimulate translation initiation mediated by HCV-like IRESes border= 
 
Chloé Mengardi ; Taran Limousin; Emiliano P. Ricci; Ricardo Soto-Rifo; Didier Decimo ...
 
 
C5-substituents of uridines and 2-thiouridines present at the wobble position of tRNA determine the formation of their keto-enol or zwitterionic forms - a factor important for accuracy of reading of guanosine at the 3"-end of the mRNA codons border= 
 
Elzbieta Sochacka ; Elzbieta Lodyga-Chruscinska; Justyna Pawlak; Marek Cypryk; Paulina Bartos ...
 
 
SF3b1 mutations associated with myelodysplastic syndromes alter the fidelity of branchsite selection in yeast border= 
 
Tucker J. Carrocci; Douglas M. Zoerner; Joshua C. Paulson; Aaron A. Hoskins
 
 
The assembly factor Erb1 functions in multiple remodeling events during 60S ribosomal subunit assembly in S. cerevisiae border= 
 
Salini Konikkat; Stephanie Biedka; John L. Woolford, Jr
 
 
USP15 regulates dynamic protein'protein interactions of the spliceosome through deubiquitination of PRP31 border= 
 
Tanuza Das; Joon Kyu Park ; Jinyoung Park; Eunji Kim; Michael Rape ...
 
 
Histone-derived piRNA biogenesis depends on the ping-pong partners Piwi5 and Ago3 in Aedes aegypti border= 
 
Erika Girardi; Pascal Miesen; Bas Pennings; Lionel Frangeul; Maria-Carla Saleh ...
 
 
Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot border= 
 
Khai K. Q. Nguyen; Yessica K. Gomez; Mona Bakhom; Amethyst Radcliffe; Phuc La ...
 
 
Structural Biology
 
 
 
Spatial confinement induces hairpins in nicked circular DNA border= 
 
Aleksandre Japaridze ; Enzo Orlandini; Kathleen Beth Smith; Lucas Gmür; Francesco Valle ...
 
 
Crystal structures of the Arabidopsis thaliana organellar RNA editing factors MORF1 and MORF9 border= 
 
Sascha Haag; Magdalena Schindler ; Leona Berndt; Axel Brennicke; Mizuki Takenaka ...
 
 
Alternative DNA structure formation in the mutagenic human c-MYC promoter border= 
 
Imee Marie A. del Mundo; Maha Zewail-Foote; Sean M. Kerwin; Karen M. Vasquez
 
 
TIA-1 RRM23 binding and recognition of target oligonucleotides border= 
 
Saboora Waris ; Sofía M. García-Mauriño; Andrew Sivakumaran; Simone A. Beckham; Fionna E. Loughlin ...
 
 
Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle border= 
 
Suna P. Gulay; Sujal Bista ; Amitabh Varshney; Serdal Kirmizialtin; Karissa Y. Sanbonmatsu ...
 
 
Ribosome-dependent Vibrio cholerae mRNAse HigB2 is regulated by a beta -strand sliding mechanism border= 
 
San Hadži; Abel Garcia-Pino; Sarah Haesaerts; Dukas Jur-nas; Kenn Gerdes ...
 
 
Synthetic Biology and Bioengineering
 
 
 
Engineering microbial phenotypes through rewiring of genetic networks border= 
 
Oliver P.F Windram; Rui T.L. Rodrigues; Sangjin Lee; Matthew Haines; Travis S. Bayer
 
 
Miscellaneous/Other
 
 
 
An in vivo reporter assay for sRNA-directed gene control in Gram-positive bacteria: identifying a novel sRNA target in Staphylococcus aureus border= 
 
Lorraine Ivain; Valérie Bordeau; Alex Eyraud; Marc Hallier; Stéphane Dreano ...
 
 
Corrigendum
 
 
 
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 ...
 
 
Activation of Sp1-mediated transcription by Rta of Epstein'Barr virus via an interaction with MCAF1 border= 
 
Li-Kwan Chang; Jian-Ying Chung ; Yi-Ren Hong; Takaya Ichimura; Mitsuyoshi Nakao ...
 
 
USP15 regulates dynamic protein'protein interactions of the spliceosome through deubiquitination of PRP31 border= 
 
Tanuza Das; Joon Kyu Park; Jinyoung Park; Eunji Kim ; Michael Rape ...
 
 
Methods Online
 
 
 
Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations border= 
 
Aleksander Szczurek; Ludger Klewes; Jun Xing; Amine Gourram; Udo Birk ...
 
 
FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome border= 
 
Valentin Wucher ; Fabrice Legeai; Benoît Hédan; Guillaume Rizk; Lætitia Lagoutte ...
 
 
HMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristics border= 
 
Haitham Ashoor; Caroline Louis-Brennetot; Isabelle Janoueix-Lerosey; Vladimir B. Bajic; Valentina Boeva
 
 
Sensitive and inexpensive digital DNA analysis by microfluidic enrichment of rolling circle amplified single-molecules border=  
 
Malte Kühnemund; Iván Hernández-Neuta; Mohd Istiaq Sharif ; Matteo Cornaglia; Martin A.M. Gijs ...
 
 
RIsearch2: suffix array-based large-scale prediction of RNA'RNA interactions and siRNA off-targets border= 
 
Ferhat Alkan; Anne Wenzel; Oana Palasca; Peter Kerpedjiev ; Anders Frost Rudebeck ...
 
 
Rapid resistome mapping using nanopore sequencing border= 
 
Eric van der Helm; Lejla Imamovic; Mostafa M. Hashim Ellabaan; Willem van Schaik; Anna Koza ...
 
 
Efficient mapping of transgene integration sites and local structural changes in Cre transgenic mice using targeted locus amplification border= 
 
Carol Cain-Hom; Erik Splinter; Max van Min; Marieke Simonis; Monique van de Heijning ...
 
 
A Semi-Protected Oligonucleotide Recombination' Assay for DNA Mismatch Repair in vivo Suggests Different Modes of Repair for Lagging Strand Mismatches border= 
 
Eric A. Josephs ; Piotr E. Marszalek
 
 
Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry border= 
 
Xuesong Shi; Peter Walker; Pehr B. Harbury; Daniel Herschlag
 
 
TSSPlant: a new tool for prediction of plant Pol II promoters border= 
 
Ilham A. Shahmuradov; Ramzan Kh. Umarov ; Victor V. Solovyev
 
 
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