Subject: Nucleic Acids Research Table of Contents for 1 June 2018 ------=_Part_1055001080.1527960705265 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1055001080.1527960705265 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Nucleic Acids Research  
Volume 46 Issue 10
 
1 June 2018
 
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NAR Breakthrough Article
 
 
 
Antisense oligonucleotides correct the familial dysautonomia splicing defect in IKBKAP transgenic mice border= 
 
Rahul Sinha; Young Jin Kim; Tomoki Nomakuchi; Kentaro Sahashi; Yimin Hua ...
 
 
Survey and Summary
 
 
 
Engineering altered protein'DNA recognition specificity border= 
 
Adam J Bogdanove; Andrew Bohm; Jeffrey C Miller; Richard D Morgan; Barry L Stoddard
 
 
Computational Biology
 
 
 
Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations border= 
 
Nina M Fischer ; Marcelo D Polêto; Jakob Steuer; David van der Spoel
 
 
Improving RNA nearest neighbor parameters for helices by going beyond the two-state model border= 
 
Aleksandar Spasic; Kyle D Berger; Jonathan L Chen ; Matthew G Seetin; Douglas H Turner ...
 
 
High throughput discovery of protein variants using proteomics informed by transcriptomics border= 
 
Shyamasree Saha; David A Matthews; Conrad Bessant
 
 
 
 
Telomere sequence content can be used to determine ALT activity in tumours border=  
 
Michael Lee; Erdahl T Teber; Oliver Holmes ; Katia Nones; Ann-Marie Patch ...
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
An upstream open reading frame (uORF) signals for cellular localization of the virulence factor implicated in pregnancy associated malaria border= 
 
Yair Fastman; Shany Assaraf; Miriam Rose; Elad Milrot ; Katherine Basore ...
 
 
Mbd2-CP2c loop drives adult-type globin gene expression and definitive erythropoiesis border= 
 
Min Young Kim; Ji Sook Kim; Seung Han Son; Chang Su Lim; Hea Young Eum ...
 
 
Increased H3K9 methylation and impaired expression of Protocadherins are associated with the cognitive dysfunctions of the Kleefstra syndrome border= 
 
Giovanni Iacono; Aline Dubos; Hamid Méziane; Marco Benevento; Ehsan Habibi ...
 
 
Tetramerization of MADS family transcription factors SEPALLATA3 and AGAMOUS is required for floral meristem determinacy in Arabidopsis border= 
 
Véronique Hugouvieux; Catarina S Silva; Agnès Jourdain; Arnaud Stigliani; Quentin Charras ...
 
 
 
 
The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome border= 
 
Joshua M Tokuda; Ren Ren ; Robert F Levendosky; Rebecca J Tay; Ming Yan ...
 
 
Coupling of replisome movement with nucleosome dynamics can contribute to the parent'daughter information transfer border= 
 
Tripti Bameta; Dibyendu Das; Ranjith Padinhateeri
 
 
Sliding of a single lac repressor protein along DNA is tuned by DNA sequence and molecular switching border= 
 
Alessia Tempestini; Carina Monico ; Lucia Gardini; Francesco Vanzi; Francesco S Pavone ...
 
 
Transcriptional and epigenetic adaptation of maize chromosomes in Oat-Maize addition lines border= 
 
Zhaobin Dong; Juan Yu; Hui Li; Wei Huang; Ling Xu ...
 
 
Genome Integrity, Repair and Replication
 
 
 
The DNA damage response activates HPV16 late gene expression at the level of RNA processing border= 
 
Kersti Nilsson; Chengjun Wu; Naoko Kajitani; Haoran Yu ; Efthymios Tsimtsirakis ...
 
 
Phosphorylation of xeroderma pigmentosum group C regulates ultraviolet-induced DNA damage repair border= 
 
Palak Shah; Baozhong Zhao; Lei Qiang; Yu-Ying He
 
 
Histone H3 lysine 36 methyltransferase mobilizes NER factors to regulate tolerance against alkylation damage in fission yeast border= 
 
Kim Kiat Lim ; Thi Thuy Trang Nguyen; Adelicia Yongling Li; Yee Phan Yeo; Ee Sin Chen
 
 
Coordination of Rad1'Rad10 interactions with Msh2'Msh3, Saw1 and RPA is essential for functional 3² non-homologous tail removal border= 
 
Robin Eichmiller ; Melisa Medina-Rivera; Rachel DeSanto; Eugen Minca; Christopher Kim ...
 
 
Complex repeat structure promotes hyper-amplification and amplicon evolution through rolling-circle replication border= 
 
Takaaki Watanabe; Hisashi Tanaka; Takashi Horiuchi
 
 
Phosphorylation by CK2 regulates MUS81/EME1 in mitosis and after replication stress border= 
 
Anita Palma; Giusj Monia Pugliese; Ivana Murfuni; Veronica Marabitti; Eva Malacaria ...
 
 
Genomics
 
 
 
The fractured landscape of RNA-seq alignment: the default in our STARs border= 
 
Sara Ballouz ; Alexander Dobin; Thomas R Gingeras; Jesse Gillis
 
 
Nucleic Acid Enzymes
 
 
 
miR-122 does not impact recognition of the HCV genome by innate sensors of RNA but rather protects the 5² end from the cellular pyrophosphatases, DOM3Z and DUSP11 border= 
 
Yalena Amador-Cañizares ; Annie Bernier; Joyce A Wilson; Selena M Sagan
 
 
Defining the impact of sumoylation on substrate binding and catalysis by thymine DNA glycosylase border= 
 
Christopher T Coey; Alexander C Drohat
 
 
The Uba4 domain interplay is mediated via a thioester that is critical for tRNA thiolation through Urm1 thiocarboxylation border=  
 
Martin Termathe; Sebastian A Leidel
 
 
RNA and RNA-protein complexes
 
 
 
A metastable rRNA junction essential for bacterial 30S biogenesis border= 
 
Indra Mani Sharma; Mollie C Rappé ; Balasubrahmanyam Addepalli; Wade W Grabow; Zhuoyun Zhuang ...
 
 
SUMOylation of the m6A-RNA methyltransferase METTL3 modulates its function border= 
 
Yuzhang Du; Guofang Hou; Hailong Zhang ; Jinzhuo Dou; Jianfeng He ...
 
 
Polyadenylation and degradation of structurally abnormal mitochondrial tRNAs in human cells border= 
 
Marina Toompuu; Tea Tuomela; Pia Laine; Lars Paulin ; Eric Dufour ...
 
 
Molecular basis of titin exon exclusion by RBM20 and the novel titin splice regulator PTB4 border= 
 
Vita Dauksaite; Michael Gotthardt
 
 
An origin of the immunogenicity of in vitro transcribed RNA border= 
 
Xin Mu; Emily Greenwald; Sadeem Ahmad; Sun Hur
 
 
Drosophila tsRNAs preferentially suppress general translation machinery via antisense pairing and participate in cellular starvation response border= 
 
Shiqi Luo ; Feng He; Junjie Luo; Shengqian Dou; Yirong Wang ...
 
 
IFIT3 and IFIT2/3 promote IFIT1-mediated translation inhibition by enhancing binding to non-self RNA border= 
 
Renata C Fleith; Harriet V Mears; Xin Yun Leong; Thomas J Sanford; Edward Emmott ...
 
 
Structural Biology
 
 
 
Snapshots of a molecular swivel in action border=  
 
Caitlin S Trejo; Ronald S Rock; W Marshall Stark ; Martin R Boocock; Phoebe A Rice
 
 
Quadruplexes in ˜Dicty': crystal structure of a four-quartet G-quadruplex formed by G-rich motif found in the Dictyostelium discoideum genome border= 
 
Aurore Guédin; Linda Yingqi Lin; Samir Armane; Laurent Lacroix ; Jean-Louis Mergny ...
 
 
The phage T4 MotA transcription factor contains a novel DNA binding motif that specifically recognizes modified DNA 
 
Maxime G Cuypers ; Rosanna M Robertson; Leslie Knipling; M Brett Waddell; Kyung Moon ...
 
 
Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge border= 
 
Markus Meier; Aniel Moya-Torres ; Natalie J Krahn; Matthew D McDougall; George L Orriss ...
 
 
Synthetic Biology and Bioengineering
 
 
 
T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures border= 
 
Samuel W Schaffter; Leopold N Green ; Joanna Schneider; Hari K K Subramanian; Rebecca Schulman ...
 
 
Methods Online
 
 
 
Easy quantification of template-directed CRISPR/Cas9 editing border=  
 
Eva K Brinkman; Arne N Kousholt; Tim Harmsen ; Christ Leemans; Tao Chen ...
 
 
GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes border= 
 
Joel A Boyd; Ben J Woodcroft; Gene W Tyson
 
 
Efficient pathway enrichment and network analysis of GWAS summary data using GSA-SNP2 border= 
 
Sora Yoon; Hai C T Nguyen ; Yun J Yoo; Jinhwan Kim; Bukyung Baik ...
 
 
De novo annotation and characterization of the translatome with ribosome profiling data border= 
 
Zhengtao Xiao; Rongyao Huang; Xudong Xing ; Yuling Chen; Haiteng Deng ...
 
 
Tn5Prime, a Tn5 based 5² capture method for single cell RNA-seq border= 
 
Charles Cole; Ashley Byrne; Anna E Beaudin; E Camilla Forsberg ; Christopher Vollmers
 
 
Collection of homozygous mutant mouse embryonic stem cells arising from autodiploidization during haploid gene trap mutagenesis border= 
 
Ayako Yamanishi; Atsushi Matsuba; Ryohei Kondo; Rie Akamatsu; Sachiyo Tanaka ...
 
 
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