Subject: Nucleic Acids Research Table of Contents for 6 September 2018 ------=_Part_1839697257.1536513449301 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1839697257.1536513449301 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Nucleic Acids Research  
Volume 46 Issue 15
 
6 September 2018
 
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Survey and Summary
 
 
 
Mechanistic insights into the regulation of transcription and transcription-coupled DNA repair by Cockayne syndrome protein B border= 
 
Erica L Boetefuer ; Robert J Lake; Hua-Ying Fan
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Time-lapse imaging of molecular evolution by high-throughput sequencing border=  
 
Nam Nguyen Quang; Clément Bouvier; Adrien Henriques ; Benoit Lelandais; Frédéric Ducongé
 
 
Preparation and characterization of manganese, cobalt and zinc DNA nanoflowers with tuneable morphology, DNA content and size border= 
 
Ysobel R Baker ; Jinfeng Chen; Jason Brown; Afaf H El-Sagheer; Philip Wiseman ...
 
 
Incorporating uracil and 5-halouracils into short peptide nucleic acids for enhanced recognition of A'U pairs in dsRNAs border= 
 
Kiran M Patil ; Desiree-Faye Kaixin Toh; Zhen Yuan; Zhenyu Meng; Zhiyu Shu ...
 
 
Real-time monitoring of DNA G-quadruplexes in living cells with a small-molecule fluorescent probe border=  
 
Suge Zhang; Hongxia Sun; Lixia Wang ; Yan Liu; Hongbo Chen ...
 
 
 
Computational Biology
 
 
 
Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking border= 
 
Lucia Coronel; Antonio Suma; Cristian Micheletti
 
 
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities border=  
 
Daniel Machado; Sergej Andrejev; Melanie Tramontano ; Kiran Raosaheb Patil
 
 
Allosterism and signal transfer in DNA border= 
 
Alexandra Balaceanu; Alberto Pérez; Pablo D Dans ; Modesto Orozco
 
 
Toward predictive R-loop computational biology: genome-scale prediction of R-loops reveals their association with complex promoter structures, G-quadruplexes and transcriptionally active enhancers border= 
 
Vladimir A Kuznetsov ; Vladyslav Bondarenko; Thidathip Wongsurawat; Surya P Yenamandra; Piroon Jenjaroenpun
 
 
 
Data Resources and Analyses
 
 
 
Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae  border= 
 
Maria G Iacovella; Michael Bremang ; Omer Basha; Luciano Giacò; Walter Carotenuto ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Casein kinase 2 mediated phosphorylation of Spt6 modulates histone dynamics and regulates spurious transcription border= 
 
Emmanuelle Gouot; Wajid Bhat; Anne Rufiange; Eric Fournier; Eric Paquet ...
 
 
Effects of histone H2B ubiquitylation on the nucleosome structure and dynamics border=  
 
Wladyslaw A Krajewski; Jiabin Li; Yali Dou
 
 
Post-transcriptional regulation of Pabpn1 by the RNA binding protein HuR border=  
 
Brittany L Phillips; Ayan Banerjee; Brenda J Sanchez ; Sergio Di Marco; Imed-Eddine Gallouzi ...
 
 
EVI1 carboxy-terminal phosphorylation is ATM-mediated and sustains transcriptional modulation and self-renewal via enhanced CtBP1 association border= 
 
Roberto Paredes ; Marion Schneider; Adam Stevens; Daniel J White; Andrew J K Williamson ...
 
 
Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility border=  
 
Akihisa Osakabe; Zdravko J Lorković; Wataru Kobayashi ; Hiroaki Tachiwana; Ramesh Yelagandula ...
 
 
The RNA helicase DDX17 controls the transcriptional activity of REST and the expression of proneural microRNAs in neuronal differentiation border= 
 
Marie-Pierre Lambert ; Sophie Terrone; Guillaume Giraud; Clara Benoit-Pilven; David Cluet ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
Chromosomal over-replication in Escherichia coli recG cells is triggered by replication fork fusion and amplified if replichore symmetry is disturbed border= 
 
Sarah L Midgley-Smith; Juachi U Dimude; Toni Taylor; Nicole M Forrester; Amy L Upton ...
 
 
Histone H1 acetylation at lysine 85 regulates chromatin condensation and genome stability upon DNA damage border=  
 
Yinglu Li; Zhiming Li; Liping Dong ; Ming Tang; Ping Zhang ...
 
 
Nucleoporin 54 contributes to homologous recombination repair and post-replicative DNA integrity border=  
 
Gonzalo Rodriguez-Berriguete; Giovanna Granata; Rathi Puliyadi ; Gaganpreet Tiwana; Remko Prevo ...
 
 
The transcription-coupled DNA repair-initiating protein CSB promotes XRCC1 recruitment to oxidative DNA damage border=  
 
Hervé Menoni; Franziska Wienholz; Arjan F Theil ; Roel C Janssens; Hannes Lans ...
 
 
Trypanosoma brucei UMSBP2 is a single-stranded telomeric DNA binding protein essential for chromosome end protection border= 
 
Olga Klebanov-Akopyan; Amartya Mishra; Galina Glousker; Yehuda Tzfati; Joseph Shlomai
 
 
 
Genomics
 
 
 
A coding and non-coding transcriptomic perspective on the genomics of human metabolic disease border= 
 
James A Timmons; Philip J Atherton ; Ola Larsson; Sanjana Sood; Ilya O Blokhin ...
 
 
Performance evaluation of pathogenicity-computation methods for missense variants border=  
 
Jinchen Li; Tingting Zhao; Yi Zhang ; Kun Zhang; Leisheng Shi ...
 
 
 
Molecular Biology
 
 
 
Single molecule tracking reveals that the bacterial SMC complex moves slowly relative to the diffusion of the chromosome border= 
 
Sonja Schibany ; Luise A K Kleine Borgmann; Thomas C Rösch; Tobias Knust; Maximilian H Ulbrich ...
 
 
The ribosomal stalk protein is crucial for the action of the conserved ATPase ABCE1 border=  
 
Hirotatsu Imai; Takaya Abe; Tomohiro Miyoshi ; Shuh-ichi Nishikawa; Kosuke Ito ...
 
 
Conditional accumulation of toxic tRNAs to cause amino acid misincorporation border=  
 
Stephanie M Zimmerman; Yoshiko Kon; Alayna C Hauke ; Bianca Y Ruiz; Stanley Fields ...
 
 
Inherited disorders of cobalamin metabolism disrupt nucleocytoplasmic transport of mRNA through impaired methylation/phosphorylation of ELAVL1/HuR border= 
 
Shyue-Fang Battaglia-Hsu ; Rose Ghemrawi; David Coelho; Natacha Dreumont; Pauline Mosca ...
 
 
 
Nucleic Acid Enzymes
 
 
 
A conserved loop'wedge motif moderates reaction site search and recognition by FEN1 border= 
 
Mark J Thompson; Victoria J B Gotham; Barbara Ciani; Jane A Grasby
 
 
Escherichia coli ItaT is a type II toxin that inhibits translation by acetylating isoleucyl-tRNAIle  border= 
 
Brendan Wilcox; Ilya Osterman ; Marina Serebryakova; Dmitry Lukyanov; Ekaterina Komarova ...
 
 
Mechanisms of template handling and pseudoknot folding in human telomerase and their manipulation to expand the sequence repertoire of processive repeat synthesis border= 
 
Aishwarya P Deshpande ; Kathleen Collins
 
 
The methyltransferase domain of the Sudan ebolavirus L protein specifically targets internal adenosines of RNA substrates, in addition to the cap structure border= 
 
Baptiste Martin; Bruno Coutard; Théo Guez; Guido C Paesen; Bruno Canard ...
 
 
 
RNA and RNA-protein complexes
 
 
 
Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort border= 
 
Raphaël Leman; Pascaline Gaildrat ; Gérald L Gac; Chandran Ka; Yann Fichou ...
 
 
Stability of local secondary structure determines selectivity of viral RNA chaperones border=  
 
Jack P K Bravo; Alexander Borodavka; Anders Barth ; Antonio N Calabrese; Peter Mojzes ...
 
 
Blocking of an intronic splicing silencer completely rescues IKBKAP exon 20 splicing in familial dysautonomia patient cells border= 
 
Gitte H Bruun; Jeanne M V Bang ; Lise L Christensen; Sabrina Brøner; Ulrika S S Petersen ...
 
 
Bidirectional regulation of adenosine-to-inosine (A-to-I) RNA editing by DEAH box helicase 9 (DHX9) in cancer border=  
 
HuiQi Hong; Omer An; Tim H M Chan ; Vanessa H E Ng; Hui Si Kwok ...
 
 
Group I introns are widespread in archaea border= 
 
Eric P Nawrocki; Thomas A Jones; Sean R Eddy
 
 
 
Structural Biology
 
 
 
Snapshots of an evolved DNA polymerase pre- and post-incorporation of an unnatural nucleotide border= 
 
Isha Singh; Roberto Laos ; Shuichi Hoshika; Steven A Benner; Millie M Georgiadis
 
 
Identification of receptors for UNCG and GNRA Z-turns and their occurrence in rRNA border=  
 
Luigi D'Ascenzo; Quentin Vicens; Pascal Auffinger
 
 
The temperature dependence of the helical twist of DNA border= 
 
Franziska Kriegel; Christian Matek; TomáÅ¡ DrÅ¡ata ; Klara Kulenkampff; Sophie Tschirpke ...
 
 
Structure of the bifunctional cryptochrome aCRY from Chlamydomonas reinhardtii border=  
 
Sophie Franz; Elisabeth Ignatz; Sandra Wenzel ; Hannah Zielosko; Eka Putra Gusti Ngurah Putu ...
 
 
 
Erratum
 
 
 
Toward predictive R-loop computational biology: genome-scale prediction of R-loops reveals their association with complex promoter structures, G-quadruplexes and transcriptionally active enhancers border= 
 
Vladimir A Kuznetsov ; Vladyslav Bondarenko; Thidathip Wongsurawat; Surya P Yenamandra; Piroon Jenjaroenpun
 
 
 
Methods Online
 
 
 
Two are better than one: HPoxBS - hairpin oxidative bisulfite sequencing border=  
 
Pascal Giehr; Charalampos Kyriakopoulos; Konstantin Lepikhov ; Stefan Wallner; Verena Wolf ...
 
 
CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data border= 
 
Wenyuan Li ; Qingjiao Li; Shuli Kang; Mary Same; Yonggang Zhou ...
 
 
Implementation of the CRISPR-Cas13a system in fission yeast and its repurposing for precise RNA editing border=  
 
Xinyun Jing; Bingran Xie; Longxian Chen ; Niubing Zhang; Yiyi Jiang ...
 
 
peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data border=  
 
Geert Geeven; Hans Teunissen; Wouter de Laat ; Elzo de Wit
 
 
Development of the variant calling algorithm, ADIScan, and its use to estimate discordant sequences between monozygotic twins border= 
 
Yangrae Cho ; Sunho Lee; Jong Hui Hong; Byong Joon Kim; Woon-Young Hong ...
 
 
Synthetic switch-based baculovirus for transgene expression control and selective killing of hepatocellular carcinoma cells border= 
 
Mei-Wei Lin ; Yen-Wen Tseng; Chih-Che Shen; Mu-Nung Hsu; Jih-Ru Hwu ...
 
 
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