Subject: Nucleic Acids Research Table of Contents for 2 June 2017 Oxford Academic
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Nucleic Acids Research  
Volume 45 Issue 10
2 June 2017
Chemical Biology and Nucleic Acid Chemistry
Synthesis and polymerase activity of a fluorescent cytidine TNA triphosphate analogue border= 
Hui Mei; Changhua Shi; Randi M. Jimenez; Yajun Wang ; Miramar Kardouh ...
Computational Biology
Global miRNA expression analysis identifies novel key regulators of plasma cell differentiation and malignant plasma cell border= 
Alboukadel Kassambara; Michel Jourdan; Angélique Bruyer; Nicolas Robert; Véronique Pantesco ...
Exploring genetic associations with ceRNA regulation in the human genome border= 
Mulin Jun Li ; Jian Zhang; Qian Liang; Chenghao Xuan; Jiexing Wu ...
Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data border= 
Mahdi Zamanighomi; Zhixiang Lin; Yong Wang; Rui Jiang; Wing Hung Wong
Data Resources and Analyses
ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data 
Christopher A. Lavender; Andrew J. Shapiro; Adam B. Burkholder; Brian D. Bennett; Karen Adelman ...
Gene Regulation, Chromatin and Epigenetics
H3.Y discriminates between HIRA and DAXX chaperone complexes and reveals unexpected insights into human DAXX-H3.3-H4 binding and deposition requirements border= 
Lisa-Maria Zink; Erwan Delbarre; H. Christian Eberl; Eva C. Keilhauer; Clemens Bönisch ...
Structural and mechanistic insights into regulation of HBO1 histone acetyltransferase activity by BRPF2 border= 
Ye Tao ; Chen Zhong; Junjun Zhu; Shutong Xu; Jianping Ding
A class of circadian long non-coding RNAs mark enhancers modulating long-range circadian gene regulation border= 
Zenghua Fan; Meng Zhao ; Parth D. Joshi; Ping Li; Yan Zhang ...
ICF-specific DNMT3B dysfunction interferes with intragenic regulation of mRNA transcription and alternative splicing border= 
Sole Gatto; Miriam Gagliardi; Monica Franzese ; Sylwia Leppert; Mariarosaria Papa ...
ChIP-seq analysis of the LuxR-type regulator VjbR reveals novel insights into the Brucella virulence gene expression network border= 
Claudia L. Kleinman; Gabriela Sycz; Hernán R. Bonomi; Romina M. Rodríguez ; Angeles Zorreguieta ...
Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells border= 
Juri Kazakevych ; Sergi Sayols; Berith Messner; Christina Krienke; Natalia Soshnikova
Trypanosoma brucei RAP1 maintains telomere and subtelomere integrity by suppressing TERRA and telomeric RNA:DNA hybrids border= 
Vishal Nanavaty; Ranjodh Sandhu ; Sanaa E. Jehi; Unnati M. Pandya; Bibo Li
New inhibitor targeting human transcription factor HSF1: effects on the heat shock response and tumor cell survival border= 
Nuria Vilaboa; Alba Boré; Francisco Martin-Saavedra ; Melanie Bayford; Natalie Winfield ...
Genome urbanization: clusters of topologically co-regulated genes delineate functional compartments in the genome of Saccharomyces cerevisiae border= 
Maria Tsochatzidou; Maria Malliarou; Nikolas Papanikolaou; Joaquim Roca ; Christoforos Nikolaou
Functional anatomy of the immunoglobulin heavy chain 3Î" super-enhancer needs not only core enhancer elements but also their unique DNA context border= 
Sandrine Le Noir; François Boyer; Sandrine Lecardeur; Mylène Brousse; Zeliha Oruc ...
Genome Integrity, Repair and Replication
Telomere associated primase Tap repairs truncated telomeres of Streptomyces border= 
Chien-Chin Yang ; Shu-Min Tseng; Hung-Yin Pan; Chih-Hung Huang; Carton W. Chen
Yeast Sub1 and human PC4 are G-quadruplex binding proteins that suppress genome instability at co-transcriptionally formed G4 DNA border= 
Christopher R. Lopez ; Shivani Singh; Shashank Hambarde; Wezley C. Griffin; Jun Gao ...
Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens : characterization of a new class of UDG with broad substrate specificity border= 
Ullas Valiya Chembazhi; Vinod Vikas Patil ; Shivjee Sah; Wayne Reeve; Ravi P. Tiwari ...
A non-catalytic role of RecBCD in homology directed gap repair and translesion synthesis border= 
Luisa Laureti; Lara Lee; Gaëlle Philippin; Vincent Pagès
The SWI/SNF ATP-dependent nucleosome remodeler promotes resection initiation at a DNA double-strand break in yeast border= 
Nathaniel E. Wiest ; Scott Houghtaling; Joseph C. Sanchez; Alan E. Tomkinson; Mary Ann Osley
DICER and ZRF1 contribute to chromatin decondensation during nucleotide excision repair border= 
Shalaka Chitale; Holger Richly
Molecular Biology
Guanine quadruplex monoclonal antibody 1H6 cross-reacts with restrained thymidine-rich single stranded DNA border= 
Hinke G. Kazemier ; Katrin Paeschke; Peter M. Lansdorp
Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers border= 
Franziska Kriegel; Niklas Ermann; Ruaridh Forbes; David Dulin ; Nynke H. Dekker ...
Identification of miRNA-7 by genome-wide analysis as a critical sensitizer for TRAIL-induced apoptosis in glioblastoma cells border= 
Xiao Zhang; Xiang Zhang; Shijie Hu; Minhua Zheng; Jie Zhang ...
Proteomic analysis of polyribosomes identifies splicing factors as potential regulators of translation during mitosis border= 
Ranen Aviner ; Sarah Hofmann; Tamar Elman; Anjana Shenoy; Tamar Geiger ...
Nucleic Acid Enzymes
A non-canonical multisubunit RNA polymerase encoded by the AR9 phage recognizes the template strand of its uracil-containing promoters border= 
Maria Sokolova ; Sergei Borukhov; Daria Lavysh; Tatjana Artamonova; Mikhail Khodorkovskii ...
The dynamics of the monomeric restriction endonuclease BcnI during its interaction with DNA border= 
Georgij Kostiuk; Jasmina Dikić ; Friedrich W. Schwarz; Giedrius Sasnauskas; Ralf Seidel ...
Downstream element determines RNase Y cleavage of the saePQRS operon in Staphylococcus aureus border= 
Gabriella Marincola; Christiane Wolz
Roles of the C-terminal domains of topoisomerase IIalpha and topoisomerase IIbeta in regulation of the decatenation checkpoint border= 
Toshiyuki Kozuki; Kenichi Chikamori; Marius D. Surleac; Marius A. Micluta; Andrei J. Petrescu ...
Coordination among tertiary base pairs results in an efficient frameshift-stimulating RNA pseudoknot border= 
Yu-Ting Chen; Kai-Chun Chang ; Hao-Teng Hu; Yi-Lan Chen; You-Hsin Lin ...
N1-methyl-pseudouridine in mRNA enhances translation through eIF2alpha -dependent and independent mechanisms by increasing ribosome density border=  
Yuri V. Svitkin; Yi Min Cheng; Tirtha Chakraborty ; Vladimir Presnyak; Matthias John ...
Comparative analyses of the thermodynamic RNA binding signatures of different types of RNA recognition motifs border= 
Brighton Samatanga; Antoine Cléry; Pierre Barraud; Frédéric H-T Allain ; Ilian Jelesarov
N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein border= 
Nian Liu; Katherine I. Zhou; Marc Parisien; Qing Dai; Luda Diatchenko ...
AUF1 facilitates microRNA-mediated gene silencing 
Kyung-Won Min; Myung Hyun Jo ; Soochul Shin; Sylvia Davila; Richard W. Zealy ...
sCLIP'an integrated platform to study RNA'protein interactomes in biomedical research: identification of CSTF2tau in alternative processing of small nuclear RNAs border=  
Yulia Kargapolova; Michal Levin; Karl Lackner ; Sven Danckwardt
RNA'protein interactions govern antiviral specificity and encapsidation of broad spectrum anti-HIV reverse transcriptase aptamers border= 
Margaret J. Lange; Phuong D. M. Nguyen; Mackenzie K. Callaway; Marc C. Johnson; Donald H. Burke
Random pseuoduridylation in vivo reveals critical region of Escherichia coli 23S rRNA for ribosome assembly border= 
Margus Leppik ; Aivar Liiv; Jaanus Remme
Melting temperature highlights functionally important RNA structure and sequence elements in yeast mRNA coding regions border= 
Fei Qi; Dmitrij Frishman
The pentatricopeptide repeat protein MTSF2 stabilizes a nad1 precursor transcript and defines the 3Î" end of its 5Î"-half intron border=  
Chuande Wang; Fabien Aubé; Noelya Planchard ; Martine Quadrado; Céline Dargel-Graffin ...
FASTKD1 and FASTKD4 have opposite effects on expression of specific mitochondrial RNAs, depending upon their endonuclease-like RAP domain border= 
Erik Boehm; Sofia Zaganelli; Kinsey Maundrell; Alexis A. Jourdain ; Stéphane Thore ...
The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq border= 
Nadja Heidrich; Saskia Bauriedl; Lars Barquist; Lei Li; Christoph Schoen ...
A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction border= 
Jeffrey Zuber; Hongying Sun; Xiaoju Zhang; Iain McFadyen; David H. Mathews
TDP-43 suppresses tau expression via promoting its mRNA instability border= 
Jianlan Gu ; Feng Wu; Wen Xu; Jianhua Shi; Wen Hu ...
Genome-wide mapping of infection-induced SINE RNAs reveals a role in selective mRNA export border= 
John Karijolich; Yang Zhao ; Ravi Alla; Britt Glaunsinger
Structural Biology
The crystal structure of Trz1, the long form RNase Z from yeast border= 
Miao Ma; Ines Li de la Sierra-Gallay; Noureddine Lazar; Olivier Pellegrini ; Dominique Durand ...
Structure of acid deoxyribonuclease border= 
Armando Varela-Ramirez; Jan Abendroth; Adrian A. Mejia; Isabelle Q. Phan; Donald D. Lorimer ...
Structural basis for the D-stereoselectivity of human DNA polymerase beta  border= 
Rajan Vyas ; Andrew J. Reed; Austin T. Raper; Walter J. Zahurancik; Petra C. Wallenmeyer ...
Structural and functional characterization of the PNKP'XRCC4'LigIV DNA repair complex border= 
R. Daniel Aceytuno; Cortt G. Piett ; Zahra Havali-Shahriari; Ross A. Edwards; Martial Rey ...
Expression of Concern
Detection of G-quadruplex DNA in mammalian cells border=  
Alexander Henderson; Yuliang Wu; Yu Chuan Huang ; Elizabeth A. Chavez; Jesse Platt ...
Guanine quadruplex structures localize to heterochromatin border= 
Roland F. Hoffmann; Yuri M. Moshkin; Stijn Mouton; Nicola A. Grzeschik ; Ruby D. Kalicharan ...
ADPriboDB: The database of ADP-ribosylated proteins border= 
Christina A. Vivelo; Ricky Wat; Charul Agrawal; Hui Yi Tee; Anthony K.L. Leung
Structural basis for the Smad5 MH1 domain to recognize different DNA sequences border= 
Nan Chai ; Wan-Xin Li; Jue Wang; Zhi-Xin Wang; Shi-Ming Yang ...
Methods Online
MosaicHunter: accurate detection of postzygotic single-nucleotide mosaicism through next-generation sequencing of unpaired, trio, and paired samples border= 
August Yue Huang ; Zheng Zhang; Adam Yongxin Ye; Yanmei Dou; Linlin Yan ...
Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells border= 
Lin Han; Hua-Jun Wu ; Haiying Zhu; Kun-Yong Kim; Sadie L. Marjani ...
Extensive libraries of gene truncation variants generated by in vitro transposition border= 
Aleardo Morelli; Yari Cabezas; Lauren J. Mills; Burckhard Seelig
Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase border= 
Marie-Theres Gansauge ; Tobias Gerber; Isabelle Glocke; Petra Korlević; Laurin Lippik ...
AssemblX: a user-friendly toolkit for rapid and reliable multi-gene assemblies border= 
Lena Hochrein; Fabian Machens ; Juergen Gremmels; Karina Schulz; Katrin Messerschmidt ...
IC-Finder: inferring robustly the hierarchical organization of chromatin folding border= 
Noelle Haddad; CĂ©dric Vaillant; Daniel Jost
Accurately annotate compound effects of genetic variants using a context-sensitive framework border= 
Si-Jin Cheng; Fang-Yuan Shi ; Huan Liu; Yang Ding; Shuai Jiang ...
BrainScope: interactive visual exploration of the spatial and temporal human brain transcriptome border= 
Sjoerd M.H. Huisman; Baldur van Lew; Ahmed Mahfouz; Nicola Pezzotti; Thomas Höllt ...
DRNApred, fast sequence-based method that accurately predicts and discriminates DNA- and RNA-binding residues border= 
Jing Yan; Lukasz Kurgan
Dynamic chromatin accessibility modeled by Markov process of randomly-moving molecules in the 3D genome border= 
Yinan Wang; Caoqi Fan; Yuxuan Zheng; Cheng Li
Discovery of cancer common and specific driver gene sets border= 
Junhua Zhang; Shihua Zhang
Removing bias against short sequences enables northern blotting to better complement RNA-seq for the study of small RNAs border= 
Yun S. Choi ; Lanelle O. Edwards; Aubrey DiBello; Antony M. Jose
An accurate and efficient method for large-scale SSR genotyping and applications border= 
Lun Li; Zhiwei Fang; Junfei Zhou; Hong Chen ; Zhangfeng Hu ...
Use of mariner transposases for one-step delivery and integration of DNA in prokaryotes and eukaryotes by transfection border= 
Maryia Trubitsyna; Gracjan Michlewski; David J. Finnegan; Alistair Elfick; Susan J. Rosser ...
A branch-migration based fluorescent probe for straightforward, sensitive and specific discrimination of DNA mutations border= 
Xianjin Xiao ; Tongbo Wu; Lei Xu; Wei Chen; Meiping Zhao
RCAS: an RNA centric annotation system for transcriptome-wide regions of interest border= 
Bora Uyar; Dilmurat Yusuf ; Ricardo Wurmus; Nikolaus Rajewsky; Uwe Ohler ...
Stabilization of RNA hairpins using non-nucleotide linkers and circularization border= 
Agnieszka Kiliszek; Leszek BĹ‚aszczyk; Ryszard Kierzek; Wojciech Rypniewski
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