Subject: Nucleic Acids Research Table of Contents for 2 June 2017 Oxford Academic
 
 
 
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New issue alert
 
Nucleic Acids Research  
Volume 45 Issue 10
 
2 June 2017
 
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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 ...
 
 
RNA
 
 
 
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 ...
 
 
Corrigendum
 
 
 
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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