Subject: Nucleic Acids Research Table of Contents for 16 November 2018 ------=_Part_1964854992.1542647342120 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1964854992.1542647342120 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Nucleic Acids Research  
Volume 46 Issue 20
 
16 November 2018
 
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NAR Breakthrough Article
 
 
 
Recombination is required for efficient HIV-1 replication and the maintenance of viral genome integrity 
 
Jonathan M O Rawson; Olga A Nikolaitchik; Brandon F Keele ; Vinay K Pathak; Wei-Shau Hu
 
 
 
Survey and Summary
 
 
 
Multi-omic and multi-view clustering algorithms: review and cancer benchmark border=  
 
Nimrod Rappoport; Ron Shamir
 
 
Viroid research and its significance for RNA technology and basic biochemistry border=  
 
Gerhard Steger; Detlev Riesner
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Mapping interfacial hydration in ETS-family transcription factor complexes with DNA: a chimeric approach border= 
 
Amanda V Albrecht; Hye Mi Kim; Gregory M K Poon
 
 
The NTP binding site of the polymerase ribozyme border= 
 
Arvin Akoopie; Ulrich F Müller
 
 
 
Computational Biology
 
 
 
Mathematical modeling identifies potential gene structure determinants of co-transcriptional control of alternative pre-mRNA splicing border= 
 
Jeremy Davis-Turak ; Tracy L Johnson; Alexander Hoffmann
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Conserved sequences in the Drosophila mod(mdg4) intron promote poly(A)-independent transcription termination and trans -splicing border= 
 
Maxim Tikhonov; Marina Utkina ; Oksana Maksimenko; Pavel Georgiev
 
 
QstR-dependent regulation of natural competence and type VI secretion in Vibrio cholerae border=  
 
Milena Jaskólska; Sandrine Stutzmann; Candice Stoudmann ; Melanie Blokesch
 
 
A piRNA utilizes HILI and HIWI2 mediated pathway to down-regulate ferritin heavy chain 1 mRNA in human somatic cells border=  
 
Sumirtha Balaratnam; Nicole West; Soumitra Basu
 
 
Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae border=  
 
Éva Hegedüs; Endre Kókai; Péter Nánási ; László Imre; László Halász ...
 
 
The Arabidopsis LDL1/2-HDA6 histone modification complex is functionally associated with CCA1/LHY in regulation of circadian clock genes border= 
 
Fu-Yu Hung ; Fang-Fang Chen; Chenlong Li; Chen Chen; You-Cheng Lai ...
 
 
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 border=  
 
Ye Gao; James T Yurkovich; Sang Woo Seo ; Ilyas Kabimoldayev; Andreas Dräger ...
 
 
Regulation of muscle atrophy-related genes by the opposing transcriptional activities of ZEB1/CtBP and FOXO3 border=  
 
Chiara Ninfali; Laura Siles; Douglas S Darling ; Antonio Postigo
 
 
Efficiency and precision of microRNA biogenesis modes in plants border= 
 
Belén Moro; Uciel Chorostecki; Siwaret Arikit ; Irina P Suarez; Claudia Höbartner ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
PLK1 targets CtIP to promote microhomology-mediated end joining border=  
 
Hailong Wang; Zhiyu Qiu; Bo Liu ; Yan Wu; Jianping Ren ...
 
 
I260Q DNA polymerase beta highlights precatalytic conformational rearrangements critical for fidelity border=  
 
Cary Liptak; Mariam M Mahmoud; Brian E Eckenroth ; Marcus V Moreno; Kyle East ...
 
 
Snapshots of archaeal DNA replication and repair in living cells using super-resolution imaging border=  
 
Floriane Delpech; Yoann Collien; Pierre Mahou ; Emmanuel Beaurepaire; Hannu Myllykallio ...
 
 
Transcript availability dictates the balance between strand-asynchronous and strand-coupled mitochondrial DNA replication border= 
 
Tricia J Cluett ; Gokhan Akman; Aurelio Reyes; Lawrence Kazak; Alice Mitchell ...
 
 
Coordinated protein and DNA conformational changes govern mismatch repair initiation by MutS border=  
 
Sharonda J LeBlanc; Jacob W Gauer; Pengyu Hao ; Brandon C Case; Manju M Hingorani ...
 
 
 
Genomics
 
 
 
Progressing super-enhancer landscape during mammary differentiation controls tissue-specific gene regulation 
 
Hye Kyung Lee; Michaela Willi; Ha Youn Shin; Chengyu Liu; Lothar Hennighausen
 
 
 
Molecular Biology
 
 
 
Controller protein of restriction'modification system Kpn2I affects transcription of its gene by acting as a transcription elongation roadblock border= 
 
Evgeny Klimuk ; Ekaterina Bogdanova; Max Nagornykh; Andjela Rodic; Marko Djordjevic ...
 
 
Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation border=  
 
David R Gruber; Joanna J Toner; Heather L Miears ; Andrey V Shernyukov; Alexey S Kiryutin ...
 
 
 
Nucleic Acid Enzymes
 
 
 
A unique intra-molecular fidelity-modulating mechanism identified in a viral RNA-dependent RNA polymerase border= 
 
Weichi Liu; Xiaoling Shi; Peng Gong
 
 
Nonfilament-forming RecA dimer catalyzes homologous joint formation border=  
 
Takeshi Shinohara; Naoto Arai; Yukari Iikura ; Motochika Kasagi; Tokiha Masuda-Ozawa ...
 
 
Active site closure stabilizes the backtracked state of RNA polymerase border=  
 
Matti Turtola; Janne J Mäkinen; Georgiy A Belogurov
 
 
MutT homologue 1 (MTH1) catalyzes the hydrolysis of mutagenic O6-methyl-dGTP border=  
 
Ann-Sofie Jemth; Robert Gustafsson; Lars Bräutigam ; Linda Henriksson; Karl S A Vallin ...
 
 
 
RNA and RNA-protein complexes
 
 
 
Functional features defining the efficacy of cholesterol-conjugated, self-deliverable, chemically modified siRNAs border= 
 
Taisia Shmushkovich ; Kathryn R Monopoli; Diana Homsy; Dmitriy Leyfer; Monica Betancur-Boissel ...
 
 
Conformational switch in the ribosomal protein S1 guides unfolding of structured RNAs for translation initiation border=  
 
Nusrat Shahin Qureshi; Jasleen Kaur Bains; Sridhar Sreeramulu ; Harald Schwalbe; Boris Fürtig
 
 
Deletion of Mtu1 (Trmu) in zebrafish revealed the essential role of tRNA modification in mitochondrial biogenesis and hearing function border= 
 
Qinghai Zhang ; Luwen Zhang; Danni Chen; Xiao He; Shihao Yao ...
 
 
How to fold and protect mitochondrial ribosomal RNA with fewer guanines border=  
 
Maryam Hosseini; Poorna Roy; Marie Sissler ; Craig L Zirbel; Eric Westhof ...
 
 
Post-transcriptional gene regulation by an Hfq-independent small RNA in Caulobacter crescentus border=  
 
Kathrin S Fröhlich; Konrad U Förstner; Zemer Gitai
 
 
High-affinity RNA targets of the Survival Motor Neuron protein reveal diverse preferences for sequence and structural motifs border= 
 
Eric W Ottesen ; Natalia N Singh; Diou Luo; Ravindra N Singh
 
 
Identification of the RNA polymerase I-RNA interactome border= 
 
David Piñeiro; Mark Stoneley; Manasa Ramakrishna ; Jana Alexandrova; Veronica Dezi ...
 
 
Small RNA sequences derived from pre-microRNAs in the supraspliceosome border=  
 
Shelly Mahlab-Aviv; Ayub Boulos; Ayelet R Peretz ; Tsiona Eliyahu; Liran Carmel ...
 
 
Non-canonical translation initiation of the spliced mRNA encoding the human T-cell leukemia virus type 1 basic leucine zipper protein border= 
 
C Joaquín Cáceres ; Jenniffer Angulo; Fernando Lowy; Nataly Contreras; Beth Walters ...
 
 
Role of ribosome assembly in Escherichia coli ribosomal RNA degradation border=  
 
Chaitanya Jain
 
 
 
Structural Biology
 
 
 
Role of aIF1 in Pyrococcus abyssi translation initiation border=  
 
Auriane Monestier; Christine Lazennec-Schurdevin; Pierre-Damien Coureux ; Yves Mechulam; Emmanuelle Schmitt
 
 
Structural insights into DNA degradation by human mitochondrial nuclease MGME1 border=  
 
Chun Yang; Ruiqi Wu; Hehua Liu ; Yiqing Chen; Yanqing Gao ...
 
 
A monovalent ion in the DNA binding interface of the eukaryotic junction-resolving enzyme GEN1 border=  
 
Yijin Liu; Alasdair DJ Freeman; Anne-Cécile Déclais ; David M J Lilley
 
 
Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA? border=  
 
Atul Rangadurai; Huiqing Zhou; Dawn K Merriman ; Nathalie Meiser; Bei Liu ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
Engineered dCas9 with reduced toxicity in bacteria: implications for genetic circuit design border= 
 
Shuyi Zhang; Christopher A Voigt
 
 
 
Corrigendum
 
 
 
A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase ' extensive moonlighting in mitochondrial tRNA biogenesis border= 
 
Elisa Vilardo ; Christa Nachbagauer; Aurélie Buzet; Andreas Taschner; Johann Holzmann ...
 
 
 
Methods Online
 
 
 
Northern lights assay: a versatile method for comprehensive detection of DNA damage border= 
 
Bjarki Gudmundsson; Hans G Thormar ; Albert Sigurdsson; Wendy Dankers; Margret Steinarsdottir ...
 
 
Impulse model-based differential expression analysis of time course sequencing data border=  
 
David S Fischer; Fabian J Theis; Nir Yosef
 
 
Umap and Bismap: quantifying genome and methylome mappability border= 
 
Mehran Karimzadeh; Carl Ernst; Anshul Kundaje ; Michael M Hoffman
 
 
Disentangling transcription factor binding site complexity border= 
 
Ralf Eggeling
 
 
TranSurVeyor: an improved database-free algorithm for finding non-reference transpositions in high-throughput sequencing data border= 
 
Ramesh Rajaby ; Wing-Kin Sung
 
 
SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions border=  
 
Wanding Zhou; Timothy J Triche, Jr; Peter W Laird ; Hui Shen
 
 
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