Subject: Nucleic Acids Research Table of Contents for 21 August 2018 ------=_Part_1307546368.1535053862148 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.mcmaster.ca. ------=_Part_1307546368.1535053862148 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Nucleic Acids Research  
Volume 46 Issue 14
 
21 August 2018
 
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NAR Breakthrough Article
 
 
 
Generating genomic platforms to study Candida albicans pathogenesis border= 
 
Mélanie Legrand; Sophie Bachellier-Bassi; Keunsook K Lee; Yogesh Chaudhari ; Hélène Tournu ...
 
 
Survey and Summary
 
 
 
Translational regulation in mycobacteria and its implications for pathogenicity border= 
 
Elizabeth B Sawyer ; Anna D Grabowska; Teresa Cortes
 
 
Initiation of homologous recombination at DNA nicks border= 
 
Nancy Maizels; Luther Davis
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
The role of spacer sequence in modulating turn-on fluorescence of DNA-templated silver nanoclusters border= 
 
Yan Shan Ang; Wei Wen Elvin Woon; Lin-Yue Lanry Yung
 
 
SHAPE probing pictures Mg2+ -dependent folding of small self-cleaving ribozymes border= 
 
Catherina Gasser; Jennifer Gebetsberger ; Manuel Gebetsberger; Ronald Micura
 
 
Solid phase chemistry to covalently and reversibly capture thiolated RNA border= 
 
Erin E Duffy; Daniele Canzio; Tom Maniatis; Matthew D Simon
 
 
Computational Biology
 
 
 
MMARGE: Motif Mutation Analysis for Regulatory Genomic Elements border= 
 
Verena M Link; Casey E Romanoski ; Dirk Metzler; Christopher K Glass
 
 
Tissue-specific DNA methylation loss during ageing and carcinogenesis is linked to chromosome structure, replication timing and cell division rates border= 
 
Marija Dmitrijeva; Stephan Ossowski; Luis Serrano; Martin H Schaefer
 
 
A pipeline for computational design of novel RNA-like topologies border= 
 
Swati Jain ; Alain Laederach; Silvia B V. Ramos; Tamar Schlick
 
 
Data Resources and Analyses
 
 
 
Improved sgRNA design in bacteria via genome-wide activity profiling border= 
 
Jiahui Guo; Tianmin Wang; Changge Guan; Bing Liu ; Cheng Luo ...
 
 
Loose ends: almost one in five human genes still have unresolved coding status border= 
 
Federico Abascal; David Juan; Irwin Jungreis; Laura Martinez; Maria Rigau ...
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
A transcriptional factor B paralog functions as an activator to DNA damage-responsive expression in archaea border= 
 
Xu Feng; Mengmeng Sun; Wenyuan Han; Yun Xiang Liang; Qunxin She
 
 
Choice of binding sites for CTCFL compared to CTCF is driven by chromatin and by sequence preference border=  
 
Philipp Bergmaier; Oliver Weth; Sven Dienstbach ; Thomas Boettger; Niels Galjart ...
 
 
Regulation of miR-34b/c-targeted gene expression program by SUMOylation 
 
Yi-Jia Li; Li Du; Grace Aldana-Masangkay; Xiuli Wang; Ryan Urak ...
 
 
MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast border= 
 
Di Luo ; Daiki Kato; Jumpei Nogami; Yasuyuki Ohkawa; Hitoshi Kurumizaka ...
 
 
DNA repair factor APLF acts as a H2A-H2B histone chaperone through binding its DNA interaction surface border= 
 
Ivan Corbeski; Klemen Dolinar; Hans Wienk; Rolf Boelens; Hugo van Ingen
 
 
Genome Integrity, Repair and Replication
 
 
 
Evolutionary rates of mammalian telomere-stability genes correlate with karyotype features and female germline expression border= 
 
Chiara Pontremoli; Diego Forni; Rachele Cagliani; Uberto Pozzoli ; Mario Clerici ...
 
 
N-terminal domain of human uracil DNA glycosylase (hUNG2) promotes targeting to uracil sites adjacent to ssDNA'dsDNA junctions border= 
 
Brian P Weiser; Gaddiel Rodriguez; Philip A Cole; James T Stivers
 
 
Effect of UV irradiation on Sulfolobus acidocaldarius and involvement of the general transcription factor TFB3 in the early UV response border= 
 
Frank Schult; Thuong N Le ; Andreas Albersmeier; Bernadette Rauch; Patrick Blumenkamp ...
 
 
The mitochondrial single-stranded DNA binding protein from S. cerevisiae, Rim1, does not form stable homo-tetramers and binds DNA as a dimer of dimers border= 
 
Saurabh P Singh; Vandna Kukshal ; Paolo De Bona; Edwin Antony; Roberto Galletto
 
 
Bacillus subtilis RarA modulates replication restart border= 
 
Begoña Carrasco; Elena M Seco; María López-Sanz ; Juan C Alonso; Silvia Ayora
 
 
Genomics
 
 
 
Cis-regulatory determinants of MyoD function border= 
 
Vahab D Soleimani; Duy Nguyen; Parameswaran Ramachandran; Gareth A Palidwor; Christopher J Porter ...
 
 
Human copy number variants are enriched in regions of low mappability border= 
 
Jean Monlong ; Patrick Cossette; Caroline Meloche; Guy Rouleau; Simon L Girard ...
 
 
Molecular Biology
 
 
 
Convergent evolution of integration site selection upstream of tRNA genes by yeast and amoeba retrotransposons border=  
 
Eva Kling; Thomas Spaller; Jana Schiefner ; Doreen Bönisch; Thomas Winckler
 
 
Intrinsically disordered domain of tumor suppressor p53 facilitates target search by ultrafast transfer between different DNA strands border= 
 
Yuji Itoh; Agato Murata; Satoshi Takahashi; Kiyoto Kamagata
 
 
Cyclic di-GMP integrates functionally divergent transcription factors into a regulation pathway for antioxidant defense border= 
 
Weihui Li; Lihua Hu; Zhiwei Xie; Hui Xu; Meng Li ...
 
 
Nucleic Acid Enzymes
 
 
 
The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp border= 
 
Diego Duchi; Abhishek Mazumder; Anssi M Malinen; Richard H Ebright ; Achillefs N Kapanidis
 
 
Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site border= 
 
Nan Cao; Kemin Tan; Thirunavukkarasu Annamalai; Andrzej Joachimiak; Yuk-Ching Tse-Dinh
 
 
Transitions in DNA polymerase beta mu s-ms dynamics related to substrate binding and catalysis 
 
Eugene F DeRose; Thomas W Kirby ; Geoffrey A Mueller; William A Beard; Samuel H Wilson ...
 
 
RNA and RNA-protein complexes
 
 
 
Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9 border= 
 
Hua Huang; Katannya Kapeli; Wenhao Jin; Yuk Peng Wong ; Thiruma Valavan Arumugam ...
 
 
The landscape of the non-canonical RNA-binding site of Gemin5 unveils a feedback loop counteracting the negative effect on translation border= 
 
Rosario Francisco-Velilla; Javier Fernandez-Chamorro; Ivan Dotu; Encarnación Martinez-Salas
 
 
Revealing the distinct folding phases of an RNA three-helix junction border= 
 
Alex Plumridge; Andrea M Katz ; George D Calvey; Ron Elber; Serdal Kirmizialtin ...
 
 
Identification of conserved, primary sequence motifs that direct retrovirus RNA fate border= 
 
Gatikrushna Singh; Brittany D Rife; Bradley Seufzer ; Marco Salemi; Aaron Rendahl ...
 
 
SRSF9 selectively represses ADAR2-mediated editing of brain-specific sites in primates border= 
 
Raghuvaran Shanmugam; Fan Zhang; Harini Srinivasan; John Lalith Charles Richard ; Kaiwen I Liu ...
 
 
Structural Biology
 
 
 
Cooperative recognition of T:T mismatch by echinomycin causes structural distortions in DNA duplex border= 
 
Pei-Ching Wu ; Shu-Ling Tzeng; Chung-ke Chang; Ya-Fen Kao; Michael J Waring ...
 
 
The crystal structure of the RsbN'σBldN complex from Streptomyces venezuelae defines a new structural class of anti-σ factor border= 
 
Maria A Schumacher; Matthew J Bush ; Maureen J Bibb; Félix Ramos-León; Govind Chandra ...
 
 
Transmission of dynamic supercoiling in linear and multi-way branched DNAs and its regulation revealed by a fluorescent G-quadruplex torsion sensor border= 
 
Ye Xia ; Ke-wei Zheng; Yi-de He; Hong-he Liu; Cui-jiao Wen ...
 
 
Tautomeric GU pairs within the molecular ribosomal grip and fidelity of decoding in bacteria border= 
 
Alexey Rozov; Philippe Wolff ; Henri Grosjean; Marat Yusupov; Gulnara Yusupova ...
 
 
Synthetic Biology and Bioengineering
 
 
 
High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis border= 
 
Derek M Mason; Cédric R Weber; Cristina Parola; Simon M Meng ; Victor Greiff ...
 
 
Engineering orthogonal synthetic timer circuits based on extracytoplasmic function σ factors border= 
 
Daniela Pinto; Stefano Vecchione; Hao Wu; Marco Mauri; Thorsten Mascher ...
 
 
Corrigendum
 
 
 
A transcriptional factor B paralog functions as an activator to DNA damage-responsive expression in archaea border= 
 
Xu Feng; Mengmeng Sun; Wenyuan Han; Yun Xiang Liang; Qunxin She
 
 
Inferring and modeling inheritance of differentially methylated changes across multiple generations border= 
 
Pascal Belleau; Astrid Deschênes; Marie-Pier Scott-Boyer ; Romain Lambrot; Mathieu Dalvai ...
 
 
The crystal structure of the RsbN'σBldN complex from Streptomyces venezuelae defines a new structural class of anti-σ factor border= 
 
Maria A Schumacher; Matthew J Bush; Maureen J Bibb; Félix Ramos-León ; Govind Chandra ...
 
 
The PXDLS linear motif regulates circadian rhythmicity through protein'protein interactions border= 
 
Moran Shalev; Rona Aviram; Yaarit Adamovich; Judith Kraut-Cohen; Tal Shamia ...
 
 
Methods Online
 
 
 
BCseq: accurate single cell RNA-seq quantification with bias correction border= 
 
Liang Chen; Sika Zheng
 
 
MeShClust: an intelligent tool for clustering DNA sequences border= 
 
Benjamin T James ; Brian B Luczak; Hani Z Girgis
 
 
A fluorescent reporter for quantification and enrichment of DNA editing by APOBEC'Cas9 or cleavage by Cas9 in living cells border= 
 
Amber St. Martin; Daniel Salamango; Artur Serebrenik; Nadine Shaban ; William L Brown ...
 
 
Inferring and modeling inheritance of differentially methylated changes across multiple generations border= 
 
Pascal Belleau; Astrid Deschênes; Marie-Pier Scott-Boyer; Romain Lambrot; Mathieu Dalvai ...
 
 
High-density functional-RNA arrays as a versatile platform for studying RNA-based interactions border= 
 
Jack O Phillips ; Louise E Butt; Charlotte A Henderson; Martin Devonshire; Jess Healy ...
 
 
Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH) border= 
 
Tslil Gabrieli; Hila Sharim; Dena Fridman; Nissim Arbib; Yael Michaeli ...
 
 
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