Subject: Nucleic Acids Research Table of Contents for 26 July 2019 ------=_Part_1319646221.1564169089244 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.mcmaster.ca. ------=_Part_1319646221.1564169089244 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Nucleic Acids Research  
Volume 47 Issue 13
 
26 July 2019
 
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Chemical Biology and Nucleic Acid Chemistry
 
 
 
Solvent viscosity facilitates replication and ribozyme catalysis from an RNA duplex in a model prebiotic process border= 
 
Christine He; Adriana Lozoya-Colinas; Isaac Gállego; Martha A Grover; Nicholas V Hud
 
 
Reactive OFF-ON type alkylating agents for higher-ordered structures of nucleic acids border=  
 
Kazumitsu Onizuka; Madoka E Hazemi; Norihiro Sato ; Gen-ichiro Tsuji; Shunya Ishikawa ...
 
 
Study of conformational transitions of i -motif DNA using time-resolved fluorescence and multivariate analysis methods border= 
 
Sanae Benabou; Cyril Ruckebusch ; Michel Sliwa; Anna Aviñó; Ramon Eritja ...
 
 
 
Computational Biology
 
 
 
Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization border= 
 
Lihua Zhang ; Shihua Zhang
 
 
Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations border= 
 
Jianzhong Chen ; Xingyu Wang; Laixue Pang; John Z H Zhang; Tong Zhu
 
 
Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro 
 
Soumitra Pal; Jan Hoinka; Teresa M Przytycka
 
 
Quantifying gene selection in cancer through protein functional alteration bias border=  
 
Nadav Brandes; Nathan Linial; Michal Linial
 
 
 
Data Resources and Analyses
 
 
 
Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes border= 
 
Daniela Ledezma-Tejeida; Luis Altamirano-Pacheco ; Vicente Fajardo; Julio Collado-Vides
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Remodeling and destabilization of chromosome 1 pericentromeric heterochromatin by SSX proteins border= 
 
Sofie Traynor; Niels Erik Møllegaard; Mikkel G Jørgensen; Nadine H Brückmann; Christina B Pedersen ...
 
 
CarD and RbpA modify the kinetics of initial transcription and slow promoter escape of the Mycobacterium tuberculosis RNA polymerase border= 
 
Drake Jensen; Ana Ruiz Manzano ; Jayan Rammohan; Christina L Stallings; Eric A Galburt
 
 
Acute depletion of CTCF directly affects MYC regulation through loss of enhancer'promoter looping border= 
 
Judith Hyle; Yang Zhang ; Shaela Wright; Beisi Xu; Ying Shao ...
 
 
RNA polymerase II-independent recruitment of SPT6L at transcription start sites in Arabidopsis border=  
 
Chen Chen; Jie Shu; Chenlong Li ; Raj K Thapa; Vi Nguyen ...
 
 
Disordered region of H3K9 methyltransferase Clr4 binds the nucleosome and contributes to its activity border=  
 
Elias Akoury; Guoli Ma; Segolene Demolin ; Cornelia Brönner; Manuel Zocco ...
 
 
A distal enhancer maintaining Hoxa1 expression orchestrates retinoic acid-induced early ESCs differentiation border=  
 
Guangsong Su; Dianhao Guo; Jun Chen ; Man Liu; Jian Zheng ...
 
 
Identification of DNA motifs that regulate DNA methylation border= 
 
Mengchi Wang; Kai Zhang; Vu Ngo ; Chengyu Liu; Shicai Fan ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
Biochemical reconstitution of UV-induced mutational processes border=  
 
Tomohiko Sugiyama; Yizhang Chen
 
 
The extruded non-template strand determines the architecture of R-loops border=  
 
Yeraldinne Carrasco-Salas; Amélie Malapert; Shaheen Sulthana ; Bastien Molcrette; Léa Chazot-Franguiadakis ...
 
 
RAD51 and mitotic function of mus81 are essential for recovery from low-dose of camptothecin in the absence of the WRN exonuclease border= 
 
Francesca Antonella Aiello ; Anita Palma; Eva Malacaria; Li Zheng; Judith L Campbell ...
 
 
Hypoosmotic stress induces R loop formation in nucleoli and ATR/ATM-dependent silencing of nucleolar transcription border=  
 
Artem K Velichko; Nadezhda V Petrova; Artem V Luzhin ; Olga S Strelkova; Natalia Ovsyannikova ...
 
 
Effective mismatch repair depends on timely control of PCNA retention on DNA by the Elg1 complex border=  
 
Lovely Jael Paul Solomon Devakumar; Christl Gaubitz; Victoria Lundblad ; Brian A Kelch; Takashi Kubota
 
 
 
Genomics
 
 
 
Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in Drosophila melanogaster  border= 
 
José Luis Villanueva-Cañas; Vivien Horvath ; Laura Aguilera; Josefa González
 
 
Coding palindromes in mitochondrial genes of Nematomorpha border= 
 
Kirill V Mikhailov; Boris D Efeykin; Alexander Y Panchin ; Dmitry A Knorre; Maria D Logacheva ...
 
 
 
Molecular Biology
 
 
 
Casein kinase 2 regulates telomere protein complex formation through Rap1 phosphorylation border= 
 
Haruna Inoue; Mayuri Horiguchi ; Kota Ono; Junko Kanoh
 
 
A Mn-sensing riboswitch activates expression of a Mn2+/Ca2+ ATPase transporter in Streptococcus border= 
 
Julia E Martin; My T Le ; Nabin Bhattarai; Daiana A Capdevila; Jiangchuan Shen ...
 
 
mRNA levels can be reduced by antisense oligonucleotides via no-go decay pathway border=  
 
Xue-hai Liang; Joshua G Nichols; Chih-Wei Hsu ; Timothy A Vickers; Stanley T Crooke
 
 
The SOXE transcription factors'SOX8, SOX9 and SOX10'share a bi-partite transactivation mechanism border=  
 
Abdul Haseeb; Véronique Lefebvre
 
 
 
Nucleic Acid Enzymes
 
 
 
Mimivirus encodes a multifunctional primase with DNA/RNA polymerase, terminal transferase and translesion synthesis activities border= 
 
Ankita Gupta ; Shailesh B Lad; Pratibha P Ghodke; P I Pradeepkumar; Kiran Kondabagil
 
 
Transcriptional supercoiling boosts topoisomerase II-mediated knotting of intracellular DNA border=  
 
Antonio Valdés; Lucia Coronel; Belén Martínez-García ; Joana Segura; Sílvia Dyson ...
 
 
DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes border=  
 
John F Marko; Paolo De Los Rios; Alessandro Barducci ; Stephan Gruber
 
 
Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase border=  
 
Lynnette N Jackson; Nicholas Chim; Changhua Shi ; John C Chaput
 
 
 
RNA and RNA-protein complexes
 
 
 
Tsr4 and Nap1, two novel members of the ribosomal protein chaperOME border=  
 
Ingrid Rössler; Julia Embacher; Benjamin Pillet ; Guillaume Murat; Laura Liesinger ...
 
 
In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs border=  
 
Lisa Marie Simon; Edoardo Morandi; Anna Luganini ; Giorgio Gribaudo; Luis Martinez-Sobrido ...
 
 
A dual role of the ribosome-bound chaperones RAC/Ssb in maintaining the fidelity of translation termination border=  
 
Anne-Sophie Gribling-Burrer; Marco Chiabudini; Ying Zhang ; Zonghao Qiu; Mario Scazzari ...
 
 
Direct role for the Drosophila GIGYF protein in 4EHP-mediated mRNA repression border=  
 
Vincenzo Ruscica; Praveen Bawankar; Daniel Peter ; Sigrun Helms; Cátia Igreja ...
 
 
A 5² fragment of Xist can sequester RNA produced from adjacent genes on chromatin border=  
 
David M Lee; Jackson B Trotman; Rachel E Cherney ; Kaoru Inoue; Megan D Schertzer ...
 
 
A post-transcriptional respiratome regulon in trypanosomes border= 
 
Anna Trenaman; Lucy Glover; Sebastian Hutchinson ; David Horn
 
 
 
Structural Biology
 
 
 
The structure of human EXD2 reveals a chimeric 3² to 5² exonuclease domain that discriminates substrates via metal coordination border= 
 
Jumi Park ; Song-Yi Lee; Hanbin Jeong; Myeong-Gyun Kang; Lindsey Van Haute ...
 
 
Structures and mechanism of transcription initiation by bacterial ECF factors border=  
 
Chengli Fang; Lingting Li; Liqiang Shen ; Jing Shi; Sheng Wang ...
 
 
Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev-binding site border=  
 
Chia-Chieh Chu; Raphael Plangger; Christoph Kreutz ; Hashim M Al-Hashimi
 
 
Extreme divergence between one-to-one orthologs: the structure of N15 Cro bound to operator DNA and its relationship to the lambda Cro complex border= 
 
Branwen M Hall ; Sue A Roberts; Matthew H J Cordes
 
 
 
Synthetic Biology and Bioengineering
 
 
 
Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins border= 
 
Michiel Vanmeert; Jamoliddin Razzokov; Muhammad Usman Mirza; Stephen D. Weeks; Guy Schepers ...
 
 
 
Corrigendum
 
 
 
Setting boundaries for genome-wide heterochromatic DNA deletions through flanking inverted repeats in Tetrahymena thermophile  border= 
 
Chih-Yi Gabriela Lin; Ju-Lan Chao ; Huai-Kuang Tsai; Douglas Chalker; Meng-Chao Yao
 
 
 
Erratum
 
 
 
Probing G-quadruplex topologies and recognition concurrently in real time and 3D using a dual-app nucleoside probe border= 
 
Ashok Nuthanakanti ; Ishtiyaq Ahmed; Saddam Y Khatik; Kayarat Saikrishnan; Seergazhi G Srivatsan
 
 
 
Methods Online
 
 
 
A tunable assay for modulators of genome-destabilizing DNA structures border=  
 
Imee M A del Mundo; Eun Jeong Cho; Kevin N Dalby ; Karen M Vasquez
 
 
CRISPRai for simultaneous gene activation and inhibition to promote stem cell chondrogenesis and calvarial bone regeneration border= 
 
Vu Anh Truong ; Mu-Nung Hsu; Nuong Thi Kieu Nguyen; Mei-Wei Lin; Chih-Che Shen ...
 
 
Cell-specific CRISPR'Cas9 activation by microRNA-dependent expression of anti-CRISPR proteins border=  
 
Mareike D Hoffmann; Sabine Aschenbrenner; Stefanie Grosse ; Kleopatra Rapti; Claire Domenger ...
 
 
Data-driven characterization of molecular phenotypes across heterogeneous sample collections border=  
 
Juha Mehtonen; Petri Pölönen; Sergei Häyrynen ; Olli Dufva; Jake Lin ...
 
 
EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences border=  
 
Xinzhou Ge; Haowen Zhang; Lingjue Xie ; Wei Vivian Li; Soo Bin Kwon ...
 
 
Accurate prediction of boundaries of high resolution topologically associated domains (TADs) in fruit flies using deep learning border= 
 
John Henderson ; Vi Ly; Shawn Olichwier; Pranik Chainani; Yu Liu ...
 
 
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