Subject: Nucleic Acids Research Table of Contents for 12 October 2018 ------=_Part_1458558450.1539623926278 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.mcmaster.ca. ------=_Part_1458558450.1539623926278 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Nucleic Acids Research  
Volume 46 Issue 18
 
12 October 2018
 
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NAR Breakthrough Article
 
 
 
3² end additions by T7 RNA polymerase are RNA self-templated, distributive and diverse in character'RNA-Seq analyses border= 
 
Yasaman Gholamalipour ; Aruni Karunanayake Mudiyanselage; Craig T Martin
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Loop permutation affects the topology and stability of G-quadruplexes border=  
 
Mingpan Cheng; Yu Cheng; Jingya Hao ; Guoqing Jia; Jun Zhou ...
 
 
Signaling specificity in the c-di-GMP-dependent network regulating antibiotic synthesis in Lysobacter border=  
 
Gaoge Xu; Sen Han; Cuimei Huo ; Ko-Hsin Chin; Shan-Ho Chou ...
 
 
Landscape of the complete RNA chemical modifications in the human 80S ribosome border=  
 
Masato Taoka; Yuko Nobe; Yuka Yamaki ; Ko Sato; Hideaki Ishikawa ...
 
 
 
Computational Biology
 
 
 
Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals border= 
 
Mark J Berger ; Aaron M Wenger; Harendra Guturu; Gill Bejerano
 
 
Growth-restricting effects of siRNA transfections: a largely deterministic combination of off-target binding and hybridization-independent competition border= 
 
Neha Daga ; Simone Eicher; Abhilash Kannan; Alain Casanova; Shyan H Low ...
 
 
 
Data Resources and Analyses
 
 
 
Global landscape of mouse and human cytokine transcriptional regulation border=  
 
Sebastian Carrasco Pro; Alvaro Dafonte Imedio; Clarissa Stephanie Santoso ; Kok Ann Gan; Jared Allan Sewell ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
MouR controls the expression of the Listeria monocytogenes Agr system and mediates virulence border= 
 
Jorge Pinheiro; Johnny Lisboa ; Rita Pombinho; Filipe Carvalho; Alexis Carreaux ...
 
 
The interplay between H2A.Z and H3K9 methylation in regulating HP1alpha binding to linker histone-containing chromatin border=  
 
Daniel P Ryan; David J Tremethick
 
 
From 1D sequence to 3D chromatin dynamics and cellular functions: a phase separation perspective border=  
 
Sirui Liu; Ling Zhang; Hui Quan ; Hao Tian; Luming Meng ...
 
 
H3K4me2 and WDR5 enriched chromatin interacting long non-coding RNAs maintain transcriptionally competent chromatin at divergent transcriptional units border= 
 
Santhilal Subhash ; Kankadeb Mishra; Vijay Suresh Akhade; Meena Kanduri; Tanmoy Mondal ...
 
 
Sequence-dependent DNA condensation as a driving force of DNA phase separation border=  
 
Hyunju Kang; Jejoong Yoo; Byeong-Kwon Sohn ; Seung-Won Lee; Hong Soo Lee ...
 
 
Characterization of the accessible genome in the human malaria parasite Plasmodium falciparum border=  
 
José Luis Ruiz; Juan J Tena; Cristina Bancells ; Alfred Cortés; José Luis Gómez-Skarmeta ...
 
 
Lytic gene expression in the temperate bacteriophage GIL01 is activated by a phage-encoded LexA homologue border=  
 
Nadine Fornelos; Douglas F Browning; Anja Pavlin ; Zdravko Podlesek; Vesna Hodnik ...
 
 
Function of TFIIIC, RNA polymerase III initiation factor, in activation and repression of tRNA gene transcription border=  
 
Małgorzata Cieśla; Ewa Skowronek; Magdalena Boguta
 
 
TIP60 represses activation of endogenous retroviral elements border= 
 
Deepa Rajagopalan; Roberto Tirado-Magallanes; Shreshtha Sailesh Bhatia ; Wen Shiun Teo; Stephanie Sian ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
A two-nuclease pathway involving RNase H1 is required for primer removal at human mitochondrial OriL border= 
 
Ali Al-Behadili; Jay P Uhler; Anna-Karin Berglund; Bradley Peter; Mara Doimo ...
 
 
SPOP promotes transcriptional expression of DNA repair and replication factors to prevent replication stress and genomic instability border= 
 
Kim Hjorth-Jensen ; Apolinar Maya-Mendoza; Nanna Dalgaard; Jón O Sigurðsson; Jiri Bartek ...
 
 
Increased levels of RECQ5 shift DNA repair from canonical to alternative pathways border=  
 
Henry C Olson; Luther Davis; Kostantin Kiianitsa ; Kevin J Khoo; Yilun Liu ...
 
 
The ATPase activity of E. coli RecA prevents accumulation of toxic complexes formed by erroneous binding to undamaged double stranded DNA border= 
 
Daniil V Gataulin; Jeffrey N Carey; Junya Li; Parisha Shah; Jennifer T Grubb ...
 
 
The somatic piRNA pathway controls germline transposition over generations border=  
 
Bridlin Barckmann; Marianne El-Barouk; Alain Pélisson ; Bruno Mugat; Blaise Li ...
 
 
Base and nucleotide excision repair facilitate resolution of platinum drugs-induced transcription blockage border=  
 
Jana Slyskova; Mariangela Sabatella; Cristina Ribeiro-Silva ; Colin Stok; Arjan F Theil ...
 
 
A mating-type mutagenesis screen identifies a zinc-finger protein required for specific DNA excision events in Paramecium  border= 
 
Simran Bhullar; Cyril Denby Wilkes ; Olivier Arnaiz; Mariusz Nowacki; Linda Sperling ...
 
 
Repair protein persistence at DNA lesions characterizes XPF defect with Cockayne syndrome features border=  
 
Mariangela Sabatella; Arjan F Theil; Cristina Ribeiro-Silva ; Jana Slyskova; Karen Thijssen ...
 
 
 
Molecular Biology
 
 
 
SOX4 can redirect TGF-beta -mediated SMAD3-transcriptional output in a context-dependent manner to promote tumorigenesis border= 
 
Stephin J Vervoort ; Ana Rita Lourenço; Ana Tufegdzic Vidakovic; Enric Mocholi; José L Sandoval ...
 
 
Widespread airway distribution and short-term phenotypic correction of cystic fibrosis pigs following aerosol delivery of piggyBac /adenovirus border= 
 
Ashley L Cooney; Brajesh K Singh ; Laura Marquez Loza; Ian M Thornell; Camilla E Hippee ...
 
 
Deacetylation of NAT10 by Sirt1 promotes the transition from rRNA biogenesis to autophagy upon energy stress border=  
 
Xiaofeng Liu; Shiying Cai; Chunfeng Zhang ; Zhenzhen Liu; Jianyuan Luo ...
 
 
 
Nucleic Acid Enzymes
 
 
 
NAD+ -dependent synthesis of a 5²-phospho-ADP-ribosylated RNA/DNA cap by RNA 2²-phosphotransferase Tpt1 border= 
 
Annum Munir; Ankan Banerjee ; Stewart Shuman
 
 
Ciprofloxacin impairs mitochondrial DNA replication initiation through inhibition of Topoisomerase 2 border=  
 
Anu Hangas; Koit Aasumets; Nina J Kekäläinen ; Mika Paloheinä; Jaakko L Pohjoismäki ...
 
 
Transposase subunit architecture and its relationship to genome size and the rate of transposition in prokaryotes and eukaryotes border= 
 
George Blundell-Hunter ; Michael Tellier; Ronald Chalmers
 
 
A protein'protein interaction underlies the molecular basis for substrate recognition by an adenosine-to-inosine RNA-editing enzyme border= 
 
Suba Rajendren ; Aidan C Manning; Haider Al-Awadi; Kentaro Yamada; Yuichiro Takagi ...
 
 
 
RNA and RNA-protein complexes
 
 
 
Coupled catabolism and anabolism in autocatalytic RNA sets border=  
 
Simon Arsène; Sandeep Ameta; Niles Lehman ; Andrew D Griffiths; Philippe Nghe
 
 
Hierarchical groove discrimination by Class I and II aminoacyl-tRNA synthetases reveals a palimpsest of the operational RNA code in the tRNA acceptor-stem bases border= 
 
Charles W Carter, Jr ; Peter R Wills
 
 
The primary transcriptome, small RNAs and regulation of antimicrobial resistance in Acinetobacter baumannii ATCC 17978 border= 
 
Carsten Kröger; Keith D MacKenzie ; Ebtihal Y Alshabib; Morgan W B Kirzinger; Danae M Suchan ...
 
 
Modulation of the HIV nucleocapsid dynamics finely tunes its RNA-binding properties during virion genesis border=  
 
Assia Mouhand; Anissa Belfetmi; Marjorie Catala ; Valéry Larue; Loussiné Zargarian ...
 
 
Template-assisted synthesis of adenine-mutagenized cDNA by a retroelement protein complex border=  
 
Sumit Handa; Yong Jiang; Sijia Tao ; Robert Foreman; Raymond F Schinazi ...
 
 
Parentally inherited long non-coding RNA Cyrano is involved in zebrafish neurodevelopment border=  
 
Mayuresh Anant Sarangdhar; Divya Chaubey; Nagesh Srikakulam ; Beena Pillai
 
 
Translocation kinetics and structural dynamics of ribosomes are modulated by the conformational plasticity of downstream pseudoknots border= 
 
Bo Wu ; Haibo Zhang; Ruirui Sun; Sijia Peng; Barry S Cooperman ...
 
 
Mud2 functions in transcription by recruiting the Prp19 and TREX complexes to transcribed genes border=  
 
Rashmi Minocha; Varvara Popova; Daria Kopytova ; Danny Misiak; Stefan Hüttelmaier ...
 
 
Double methylation of tRNA-U54 to 2²-O-methylthymidine (Tm) synergistically decreases immune response by Toll-like receptor 7 border= 
 
Patrick Keller ; Isabel Freund; Virginie Marchand; Guillaume Bec; Raven Huang ...
 
 
miR-122, small RNA annealing and sequence mutations alter the predicted structure of the Hepatitis C virus 5² UTR RNA to stabilize and promote viral RNA accumulation border= 
 
Yalena Amador-Cañizares ; Mamata Panigrahi; Adam Huys; Rasika D Kunden; Halim M Adams ...
 
 
 
Structural Biology
 
 
 
Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature border= 
 
Mary E O'Sullivan; Frédéric Poitevin; Raymond G Sierra; Cornelius Gati; E Han Dao ...
 
 
Molecular organization of the type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2 border=  
 
Donghyun Ka; Dong Man Jang; Byung Woo Han ; Euiyoung Bae
 
 
p15PAF binding to PCNA modulates the DNA sliding surface border=  
 
Matteo De March; Susana Barrera-Vilarmau; Emmanuele Crespan ; Elisa Mentegari; Nekane Merino ...
 
 
Activity and structure of EcoKMcrA border= 
 
Honorata Czapinska; Monika Kowalska; Evelina ZagorskaitÄ- ; Elena Manakova; Anton Slyvka ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
Programmable T7-based synthetic transcription factors border=  
 
Brendan J Hussey; David R McMillen
 
 
Synthetic control systems for high performance gene expression in mammalian cells border=  
 
Gabriele Lillacci; Yaakov Benenson; Mustafa Khammash
 
 
A synthetic free fatty acid-regulated transgene switch in mammalian cells and mice border=  
 
Ying Liu; Ghislaine Charpin-El Hamri; Haifeng Ye ; Martin Fussenegger
 
 
Synthetic negative feedback circuits using engineered small RNAs border= 
 
Ciarán L Kelly; Andreas W K Harris; Harrison Steel ; Edward J Hancock; John T Heap ...
 
 
 
Corrigendum
 
 
 
Mud2 functions in transcription by recruiting the Prp19 and TREX complexes to transcribed genes border= 
 
Rashmi Minocha; Varvara Popova ; Daria Kopytova; Danny Misiak; Stefan Hüttelmaier ...
 
 
SPOP promotes transcriptional expression of DNA repair and replication factors to prevent replication stress and genomic instability border= 
 
Kim Hjorth-Jensen ; Apolinar Maya-Mendoza; Nanna Dalgaard; Jón O Sigurðsson; Jiri Bartek ...
 
 
5-Formylcytosine mediated DNA'protein cross-links block DNA replication and induce mutations in human cells border=  
 
Shaofei Ji; Iwen Fu; Spandana Naldiga ; Hongzhao Shao; Ashis K Basu ...
 
 
Replication-dependent histone isoforms: a new source of complexity in chromatin structure and function border=  
 
Rajbir Singh; Emily Bassett; Arnab Chakravarti ; Mark R Parthun
 
 
 
Methods Online
 
 
 
Exploiting CRISPR'Cas9 technology to investigate individual histone modifications border= 
 
Juan-José Vasquez; Carolin Wedel ; Raul O Cosentino; T Nicolai Siegel
 
 
CGT-seq: epigenome-guided de novo assembly of the core genome for divergent populations with large genome border=  
 
Meifang Qi; Zijuan Li; Chunmei Liu ; Wenyan Hu; Luhuan Ye ...
 
 
TAMRA-polypyrrole for A/T sequence visualization on DNA molecules border= 
 
Seonghyun Lee; Yusuke Kawamoto; Thangavel Vaijayanthi ; Jihyun Park; Jaeyoung Bae ...
 
 
Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events border= 
 
Zhiyu Xu ; Long Hu; Binbin Shi; SiSi Geng; Longchen Xu ...
 
 
SRB-2: a promiscuous rainbow aptamer for live-cell RNA imaging border= 
 
Murat Sunbul; Andres Jäschke
 
 
A universal gene expression system for fungi border= 
 
Anssi Rantasalo; Christopher P Landowski; Joosu Kuivanen ; Annakarin Korppoo; Lauri Reuter ...
 
 
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