Subject: Nucleic Acids Research Table of Contents for 05 September 2019 ------=_Part_1483187418.1567192786273 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.mcmaster.ca. ------=_Part_1483187418.1567192786273 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Nucleic Acids Research  
Volume 47 Issue 15
 
05 September 2019
 
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NAR Breakthrough Article
 
 
 
The human 18S rRNA m6 A methyltransferase METTL5 is stabilized by TRMT112 border= 
 
Nhan van Tran; Felix G M Ernst ; Ben R Hawley; Christiane Zorbas; Nathalie Ulryck ...
 
 
 
Survey and Summary
 
 
 
DAXX in cancer: phenomena, processes, mechanisms and regulation border=  
 
Iqbal Mahmud; Daiqing Liao
 
 
Systems biology-based investigation of cooperating microRNAs as monotherapy or adjuvant therapy in cancer border=  
 
Xin Lai; Martin Eberhardt; Ulf Schmitz ; Julio Vera
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
DNA complexes with human apurinic/apyrimidinic endonuclease 1: structural insights revealed by pulsed dipolar EPR with orthogonal spin labeling border= 
 
Olesya A Krumkacheva ; Georgiy Yu Shevelev; Alexander A Lomzov; Nadezhda S Dyrkheeva; Andrey A Kuzhelev ...
 
 
 
Computational Biology
 
 
 
DNA sequence models of genome-wide Drosophila melanogaster Polycomb binding sites improve generalization to independent Polycomb Response Elements border= 
 
Bjørn André Bredesen; Marc Rehmsmeier
 
 
Weaving DNA strands: structural insight on ATP hydrolysis in RecA-induced homologous recombination border= 
 
Benjamin Boyer; Claudia Danilowicz; Mara Prentiss; Chantal Prévost
 
 
Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework border=  
 
Jinyu Yang; Anjun Ma; Adam D Hoppe ; Cankun Wang; Yang Li ...
 
 
 
Data Resources and Analyses
 
 
 
ChIP-exo analysis highlights Fkh1 and Fkh2 transcription factors as hubs that integrate multi-scale networks in budding yeast border= 
 
Thierry D G A Mondeel ; Petter Holland; Jens Nielsen; Matteo Barberis
 
 
An expanded landscape of human long noncoding RNA border= 
 
Shuai Jiang; Si-Jin Cheng; Li-Chen Ren ; Qian Wang; Yu-Jian Kang ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
The effects of Arabidopsis genome duplication on the chromatin organization and transcriptional regulation border= 
 
Hui Zhang; Ruiqin Zheng ; Yunlong Wang; Yu Zhang; Ping Hong ...
 
 
SIRT7 mediates L1 elements transcriptional repression and their association with the nuclear lamina border= 
 
Berta N Vazquez; Joshua K Thackray; Nicolas G Simonet; Sanjay Chahar; Noriko Kane-Goldsmith ...
 
 
Spliceosome disassembly factors ILP1 and NTR1 promote miRNA biogenesis in Arabidopsis thaliana border=  
 
Junli Wang; Susu Chen; Ning Jiang ; Ning Li; Xiaoyan Wang ...
 
 
CNBP controls transcription by unfolding DNA G-quadruplex structures border=  
 
Aldana P David; Angélique Pipier; Federico Pascutti ; Andrés Binolfi; Andrea M J Weiner ...
 
 
SIRT6 promotes transcription of a subset of NRF2 targets by mono-ADP-ribosylating BAF170 
 
Sarallah Rezazadeh; David Yang; Gregory Tombline; Matthew Simon ; Sean P Regan ...
 
 
Regulation of bistability in the std fimbrial operon of Salmonella enterica by DNA adenine methylation and transcription factors HdfR, StdE and StdF border= 
 
Lucía García-Pastor; María A Sánchez-Romero; Marcello Jakomin; Elena Puerta-Fernández; Josep Casadesús
 
 
The nucleosome position-encoding WW/SS sequence pattern is depleted in mammalian genes relative to other eukaryotes border=  
 
Gregory M Wright; Feng Cui
 
 
 
Genome Integrity, Repair and Replication
 
 
 
Highly efficient editing of the beta -globin gene in patient-derived hematopoietic stem and progenitor cells to treat sickle cell disease border= 
 
So Hyun Park ; Ciaran M Lee; Daniel P Dever; Timothy H Davis; Joab Camarena ...
 
 
A kinetochore-based ATM/ATR-independent DNA damage checkpoint maintains genomic integrity in trypanosomes border=  
 
Qing Zhou; Kieu T M Pham; Huiqing Hu ; Yasuhiro Kurasawa; Ziyin Li
 
 
Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair border= 
 
Wei Chen ; Aaron McKenna; Jacob Schreiber; Maximilian Haeussler; Yi Yin ...
 
 
Proteomic characterization of chromosomal common fragile site (CFS)-associated proteins uncovers ATRX as a regulator of CFS stability border= 
 
David Pladevall-Morera ; Stephanie Munk; Andreas Ingham; Lorenza Garribba; Eliene Albers ...
 
 
Double-strand breaks in ribosomal RNA genes activate a distinct signaling and chromatin response to facilitate nucleolar restructuring and repair border= 
 
Lea M Korsholm ; Zita Gál; Lin Lin; Oliver Quevedo; Diana A Ahmad ...
 
 
 
Genomics
 
 
 
Exogenous RNAi mechanisms contribute to transcriptome adaptation by phased siRNA clusters in Paramecium  border= 
 
Sivarajan Karunanithi; Vidya Oruganti ; Simone Marker; Angela M Rodriguez-Viana; Franziska Drews ...
 
 
mu LAS technology for DNA isolation coupled to Cas9-assisted targeting for sequencing and assembly of a 30 kb region in plant genome border= 
 
Nicolas Milon ; Céline Chantry-Darmon; Carine Satge; Margaux-Alison Fustier; Stephane Cauet ...
 
 
 
Molecular Biology
 
 
 
The role of ZAP and OAS3/RNAseL pathways in the attenuation of an RNA virus with elevated frequencies of CpG and UpA dinucleotides border= 
 
Valerie Odon ; Jelke J Fros; Niluka Goonawardane; Isabelle Dietrich; Ahmad Ibrahim ...
 
 
TERC promotes cellular inflammatory response independent of telomerase border=  
 
Haiying Liu; Yiding Yang; Yuanlong Ge ; Juanhong Liu; Yong Zhao
 
 
ULK1 phosphorylates Mad1 to regulate spindle assembly checkpoint border= 
 
Fengjie Yuan; Ximin Jin; Dan Li ; Yuanshuai Song; Nan Zhang ...
 
 
A hidden human proteome encoded by śnon-coding' genes border= 
 
Shaohua Lu; Jing Zhang; Xinlei Lian ; Li Sun; Kun Meng ...
 
 
 
Nucleic Acid Enzymes
 
 
 
Targeted DNA transposition in vitro using a dCas9-transposase fusion protein border= 
 
Shivam Bhatt; Ronald Chalmers
 
 
DNA processing by the MOBH family relaxase TraI encoded within the gonococcal genetic island border=  
 
Jan-Hendrik Heilers; Jens Reiners; Eva-Maria Heller ; Annika Golzer; Sander H J Smits ...
 
 
From general base to general acid catalysis in a sodium-specific DNAzyme by a guanine-to-adenine mutation border=  
 
Lingzi Ma; Sanjana Kartik; Biwu Liu ; Juewen Liu
 
 
A complex suite of loci and elements in eukaryotic type II topoisomerases determine selective sensitivity to distinct poisoning agents border= 
 
Tim R Blower ; Afif Bandak; Amy S Y Lee; Caroline A Austin; John L Nitiss ...
 
 
 
RNA and RNA-protein complexes
 
 
 
The glucocorticoid receptor DNA-binding domain recognizes RNA hairpin structures with high affinity 
 
Nicholas V Parsonnet; Nickolaus C Lammer; Zachariah E Holmes ; Robert T Batey; Deborah S Wuttke
 
 
A DEAD-box protein regulates ribosome assembly through control of ribosomal protein synthesis border=  
 
Isabelle Iost; Chaitanya Jain
 
 
Characterization of the stimulators of protein-directed ribosomal frameshifting in Theiler's murine encephalomyelitis virus border= 
 
Sawsan Napthine ; Susanne Bell; Chris H Hill; Ian Brierley; Andrew E Firth
 
 
DEAD-box helicase eIF4A2 inhibits CNOT7 deadenylation activity border= 
 
Hedda A Meijer; Tobias Schmidt; Sarah L Gillen ; Claudia Langlais; Rebekah Jukes-Jones ...
 
 
XAB2 depletion induces intron retention in POLR2A to impair global transcription and promote cellular senescence border=  
 
Shuai Hou; Dajun Qu; Yue Li ; Baohui Zhu; Dapeng Liang ...
 
 
A conserved RNA structure is essential for a satellite RNA-mediated inhibition of helper virus accumulation border=  
 
Lu He; Qian Wang; Zhouhang Gu ; Qiansheng Liao; Peter Palukaitis ...
 
 
 
Structural Biology
 
 
 
NMR solution and X-ray crystal structures of a DNA molecule containing both right- and left-handed parallel-stranded G-quadruplexes border= 
 
Fernaldo Richtia Winnerdy ; Bla┼ż Bakalar; Arijit Maity; J Jeya Vandana; Yves Mechulam ...
 
 
Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changes border= 
 
Jakub Zeman ; Yuzuru Itoh; Zden─Ťk Kuka─Źka; Michal Ros┼»lek; Daniel Kavan ...
 
 
Role of Era in assembly and homeostasis of the ribosomal small subunit border=  
 
Aida Razi; Joseph H Davis; Yumeng Hao ; Dushyant Jahagirdar; Brett Thurlow ...
 
 
Insights into the G-rich VEGF-binding aptamer V7t1: when two G-quadruplexes are better than one! border=  
 
Federica Moccia; Claudia Riccardi; Domenica Musumeci ; Serena Leone; Rosario Oliva ...
 
 
 
Corrigendum
 
 
 
Proteomic characterization of chromosomal common fragile site (CFS)-associated proteins uncovers ATRX as a regulator of CFS stability border= 
 
David Pladevall-Morera ; Stephanie Munk; Andreas Ingham; Lorenza Garribba; Eliene Albers ...
 
 
Metal sensing and regulation of adaptive responses to manganese limitation by MtsR is critical for group A streptococcus virulence border= 
 
Hackwon Do ; Nishanth Makthal; Pete Chandrangsu; Randall J Olsen; John D Helmann ...
 
 
COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis border=  
 
Charles D Warden; Heehyoung Lee; Joshua D Tompkins ; Xiaojin Li; Charles Wang ...
 
 
 
Methods Online
 
 
 
Highly efficient single-stranded DNA ligation technique improves low-input whole-genome bisulfite sequencing by post-bisulfite adaptor tagging border= 
 
Fumihito Miura ; Yukiko Shibata; Miki Miura; Yuhei Sangatsuda; Osamu Hisano ...
 
 
The dynamics of forming a triplex in an artificial telomere inferred by DNA mechanics border=  
 
Ning Li; Junli Wang; Kangkang Ma ; Lin Liang; Lipei Mi ...
 
 
High efficiency error suppression for accurate detection of low-frequency variants border=  
 
Ting Ting Wang; Sagi Abelson; Jinfeng Zou ; Tiantian Li; Zhen Zhao ...
 
 
APERO: a genome-wide approach for identifying bacterial small RNAs from RNA-Seq data border=  
 
Simon Leonard; Sam Meyer; Stephan Lacour ; William Nasser; Florence Hommais ...
 
 
Enzyme-free optical DNA mapping of the human genome using competitive binding border=  
 
Vilhelm Müller; Albertas Dvirnas; John Andersson ; Vandana Singh; Sriram KK ...
 
 
Profiling the genome-wide landscape of tandem repeat expansions border= 
 
Nima Mousavi; Sharona Shleizer-Burko; Richard Yanicky ; Melissa Gymrek
 
 
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