Subject: Nucleic Acids Research Table of Contents for 18 May 2018 Oxford Academic
 
 
 
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Nucleic Acids Research  
Volume 46 Issue 9
 
18 May 2018
 
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NAR Breakthrough Article
 
 
 
The arginine methyltransferase CARM1 represses p300¢ACT¢CREMÏ" activity and is required for spermiogenesis border= 
 
Jianqiang Bao; Sophie Rousseaux; Jianjun Shen; Kevin Lin ; Yue Lu ...
 
 
Computational Biology
 
 
 
Dehydrated DNA in B-form: ionic liquids in rescue border= 
 
Debostuti Ghoshdastidar; Sanjib Senapati
 
 
The number of titrated microRNA species dictates ceRNA regulation border= 
 
Hua-Sheng Chiu; María Rodríguez Martínez; Elena V . Komissarova; David Llobet-Navas ; Mukesh Bansal ...
 
 
Data Resources and Analyses
 
 
 
Dissecting the sources of gene expression variation in a pan-cancer analysis identifies novel regulatory mutations border= 
 
Anchal Sharma; Chuan Jiang; Subhajyoti De
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Implications of CpG islands on chromosomal architectures and modes of global gene regulation border= 
 
Samuel Beck; Catherine Rhee ; Jawon Song; Bum-Kyu Lee; Lucy LeBlanc ...
 
 
 
 
Stabilization of the methyl-CpG binding protein ZBTB38 by the deubiquitinase USP9X limits the occurrence and toxicity of oxidative stress in human cells border= 
 
Benoit Miotto; Claire Marchal; Guillaume Adelmant; Nadège Guinot; Ping Xie ...
 
 
Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance border= 
 
Robert M Vaughan; Bradley M Dickson; Evan M Cornett; Joseph S Harrison; Brian Kuhlman ...
 
 
Protein-mediated loops in supercoiled DNA create large topological domains border= 
 
Yan Yan ; Yue Ding; Fenfei Leng; David Dunlap; Laura Finzi
 
 
The IL-4/STAT6/PPARgamma signaling axis is driving the expansion of the RXR heterodimer cistrome, providing complex ligand responsiveness in macrophages border= 
 
Bence Daniel ; Gergely Nagy; Attila Horvath; Zsolt Czimmerer; Ixchelt Cuaranta-Monroy ...
 
 
Chromatin assembly factor-1 (CAF-1) chaperone regulates Cse4 deposition into chromatin in budding yeast border= 
 
Geetha S Hewawasam; Karthik Dhatchinamoorthy; Mark Mattingly; Chris Seidel; Jennifer L Gerton
 
 
 
 
Designer epigenome modifiers enable robust and sustained gene silencing in clinically relevant human cells border= 
 
Tafadzwa Mlambo; Sandra Nitsch; Markus Hildenbeutel; Marianna Romito ; Maximilian Müller ...
 
 
DNA template sequence control of bacterial RNA polymerase escape from the promoter border= 
 
Ewa Heyduk; Tomasz Heyduk
 
 
Genome Integrity, Repair and Replication
 
 
 
ATF7 mediates TNF-alpha 'induced telomere shortening border= 
 
Toshio Maekawa; Binbin Liu; Daisuke Nakai; Keisuke Yoshida ; Ken-ichi Nakamura ...
 
 
Pseudomonas aeruginosa MutL promotes large chromosomal deletions through non-homologous end joining to prevent bacteriophage predation border= 
 
Mengyu Shen; Huidong Zhang; Wei Shen; Zhenyu Zou; Shuguang Lu ...
 
 
Overexpression of the base excision repair NTHL1 glycosylase causes genomic instability and early cellular hallmarks of cancer 
 
Kristin L Limpose ; Kelly S Trego; Zhentian Li; Sara W Leung; Altaf H Sarker ...
 
 
Human RTEL1 stabilizes long G-overhangs allowing telomerase-dependent over-extension border= 
 
Rosa M Porreca; Galina Glousker ; Aya Awad; Maria I Matilla Fernandez; Anne Gibaud ...
 
 
An E2F7-dependent transcriptional program modulates DNA damage repair and genomic stability border= 
 
Jone Mitxelena; Aintzane Apraiz; Jon Vallejo-Rodríguez ; Iraia García-Santisteban; Asier Fullaondo ...
 
 
RNA-splicing factor SART3 regulates translesion DNA synthesis border= 
 
Min Huang; Bo Zhou; Juanjuan Gong; Lingyu Xing ; Xiaolu Ma ...
 
 
Genomics
 
 
 
The exon'intron gene structure upstream of the initiation codon predicts translation efficiency border= 
 
Chun Shen Lim; Samuel J T. Wardell; Torsten Kleffmann; Chris M Brown
 
 
Molecular Biology
 
 
 
Pseudomonas aeruginosa partitioning protein ParB acts as a nucleoid-associated protein binding to multiple copies of a parS-related motif border= 
 
Adam Kawalek ; Aneta A Bartosik; Krzysztof Glabski; Grazyna Jagura-Burdzy
 
 
Translatome analysis at the egg-to-embryo transition in sea urchin border= 
 
Héloïse Chassé; Julie Aubert; Sandrine Boulben ; Gildas Le Corguillé; Erwan Corre ...
 
 
Visualizing structure-mediated interactions in supercoiled DNA molecules border= 
 
Shane Scott; Zhi Ming Xu; Fedor Kouzine; Daniel J Berard ; Cynthia Shaheen ...
 
 
The nonstop decay and the RNA silencing systems operate cooperatively in plants border= 
 
István Szádeczky-Kardoss; Tibor Csorba; Andor Auber; Anita Schamberger; Tünde Nyikó ...
 
 
Nucleic Acid Enzymes
 
 
 
Mu transpososome activity-profiling yields hyperactive MuA variants for highly efficient genetic and genome engineering border= 
 
Tiina S Rasila; Elsi Pulkkinen; Saija Kiljunen; Saija Haapa-Paananen; Maria I Pajunen ...
 
 
A natural non-Watson'Crick base pair in human mitochondrial tRNAThr causes structural and functional susceptibility to local mutations border= 
 
Yong Wang; Qi-Yu Zeng; Wen-Qiang Zheng; Quan-Quan Ji; Xiao-Long Zhou ...
 
 
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 with improved proof-reading enhances homology-directed repair border= 
 
Tomoko Kato-Inui; Gou Takahashi; Szuyin Hsu; Yuichiro Miyaoka
 
 
Multiple RPAs make WRN syndrome protein a superhelicase border= 
 
Mina Lee; Soochul Shin ; Heesoo Uhm; Heesun Hong; Jaewon Kirk ...
 
 
RNA and RNA-protein complexes
 
 
 
Turnover of aberrant pre-40S pre-ribosomal particles is initiated by a novel endonucleolytic decay pathway border= 
 
Elodie Choque; Claudia Schneider; Olivier Gadal; Christophe Dez
 
 
Ribosomal protein L14 contributes to the early assembly of 60S ribosomal subunits in Saccharomyces cerevisiae border= 
 
Francisco Espinar-Marchena; Olga Rodríguez-Galán; José Fernández-Fernández; Jan Linnemann ; Jesús de la Cruz
 
 
Discovery of new type I toxin'antitoxin systems adjacent to CRISPR arrays in Clostridium difficile border= 
 
Anna Maikova; Johann Peltier; Pierre Boudry; Eliane Hajnsdorf; Nicolas Kint ...
 
 
Protein composition of catalytically active U7-dependent processing complexes assembled on histone pre-mRNA containing biotin and a photo-cleavable linker border= 
 
Aleksandra Skrajna; Xiao-cui Yang; Michał Dadlez; William F Marzluff; Zbigniew Dominski
 
 
Expanding RNA binding specificity and affinity of engineered PUF domains border= 
 
Yang-Yang Zhao ; Miao-Wei Mao; Wen-Jing Zhang; Jue Wang; Hai-Tao Li ...
 
 
De novo discovery of structural motifs in RNA 3D structures through clustering border= 
 
Ping Ge; Shahidul Islam ; Cuncong Zhong; Shaojie Zhang
 
 
A regulatory RNA is involved in RNA duplex formation and biofilm regulation in Sulfolobus acidocaldarius border= 
 
Alvaro Orell; Vanessa Tripp; Victor Aliaga-Tobar; Sonja-Verena Albers ; Vinicius Maracaja-Coutinho ...
 
 
Structural Biology
 
 
 
Crystal structure of the novel lesion-specific endonuclease PfuEndoQ from Pyrococcus furiosus border= 
 
Ken-ichi Miyazono; Sonoko Ishino; Naruto Makita; Tomoko Ito; Yoshizumi Ishino ...
 
 
Crystal structures of thrombin in complex with chemically modified thrombin DNA aptamers reveal the origins of enhanced affinity border= 
 
Rafal Dolot; Curtis H Lam; Malgorzata Sierant; Qiang Zhao; Feng-Wu Liu ...
 
 
Corrigendum
 
 
 
Chromatin assembly factor-1 (CAF-1) chaperone regulates Cse4 deposition into chromatin in budding yeast border= 
 
Geetha S Hewawasam; Karthik Dhatchinamoorthy; Mark Mattingly; Chris Seidel; Jennifer L Gerton
 
 
Methods Online
 
 
 
Phage display peptide libraries: deviations from randomness and correctives border=  
 
Arie Ryvkin; Haim Ashkenazy; Yael Weiss-Ottolenghi ; Chen Piller; Tal Pupko ...
 
 
Octopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data border= 
 
Taemook Kim; Hogyu David Seo; Lothar Hennighausen; Daeyoup Lee ; Keunsoo Kang
 
 
Improving the value of public RNA-seq expression data by phenotype prediction border= 
 
Shannon E Ellis; Leonardo Collado-Torres; Andrew Jaffe; Jeffrey T Leek
 
 
High-throughput construction of multiple cas9 gene variants via assembly of high-depth tiled and sequence-verified oligonucleotides border= 
 
Namjin Cho; Han Na Seo ; Taehoon Ryu; Euijin Kwon; Sunghoon Huh ...
 
 
Determination of an effective scoring function for RNA'RNA interactions with a physics-based double-iterative method border= 
 
Yumeng Yan; Zeyu Wen; Di Zhang ; Sheng-You Huang
 
 
In cell mutational interference mapping experiment (in cell MIME) identifies the 5² polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging border= 
 
Redmond P Smyth; Maureen R Smith; Anne-Caroline Jousset; Laurence Despons ; Géraldine Laumond ...
 
 
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