Subject: Nucleic Acids Research Table of Contents for 19 September 2018 ------=_Part_53874351.1537642066184 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.mcmaster.ca. ------=_Part_53874351.1537642066184 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Nucleic Acids Research  
Volume 46 Issue 16
 
19 September 2018
 
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Survey and Summary
 
 
 
Insights into the development of chemical probes for RNA border=  
 
Brittany S Morgan; Jordan E Forte; Amanda E Hargrove
 
 
i-Motif DNA: structural features and significance to cell biology border= 
 
Hala Abou Assi; Miguel Garavís; Carlos González ; Masad J Damha
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
In vitro selection of an XNA aptamer capable of small-molecule recognition border= 
 
Alexandra E Rangel; Zhe Chen ; Tewoderos M Ayele; Jennifer M Heemstra
 
 
A strongly pairing fifth base: oligonucleotides with a C-nucleoside replacing thymidine border=  
 
Tanja J Walter; Clemens Richert
 
 
Small synthetic molecule-stabilized RNA pseudoknot as an activator for '1 ribosomal frameshifting border=  
 
Saki Matsumoto; Neva Caliskan; Marina V Rodnina ; Asako Murata; Kazuhiko Nakatani
 
 
Structural basis for the synergy of 4²- and 2²-modifications on siRNA nuclease resistance, thermal stability and RNAi activity border= 
 
Joel M Harp ; Dale C Guenther; Anna Bisbe; Lydia Perkins; Shigeo Matsuda ...
 
 
 
Computational Biology
 
 
 
A deep recurrent neural network discovers complex biological rules to decipher RNA protein-coding potential border= 
 
Steven T Hill; Rachael Kuintzle; Amy Teegarden; Erich Merrill, III; Padideh Danaee ...
 
 
A genome-wide scan for correlated mutations detects macromolecular and chromatin interactions in Arabidopsis thaliana  border= 
 
Laura Perlaza-Jiménez; Dirk Walther
 
 
AptaBlocks: Designing RNA complexes and accelerating RNA-based drug delivery systems 
 
Yijie Wang; Jan Hoinka; Yong Liang; Tomasz Adamus ; Piotr Swiderski ...
 
 
Characterizing the 3D structure and dynamics of chromosomes and proteins in a common contact matrix framework border=  
 
Richard J Lindsay; Bill Pham; Tongye Shen ; Rachel Patton McCord
 
 
 
Data Resources and Analyses
 
 
 
Revealing a human p53 universe 
 
Thuy-Ai T Nguyen; Sara A Grimm; Pierre R Bushel; Jianying Li ; Yuanyuan Li ...
 
 
Circular RNA expression in human hematopoietic cells is widespread and cell-type specific border=  
 
Benoit P Nicolet; Sander Engels; Francesca Aglialoro ; Emile van den Akker; Marieke von Lindern ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
The sequence features that define efficient and specific hAGO2-dependent miRNA silencing guides border= 
 
Yifei Yan; Mariana Acevedo ; Lian Mignacca; Philippe Desjardins; Nicolas Scott ...
 
 
Histone variant H2A.Z deposition and acetylation directs the canonical Notch signaling response border=  
 
Benedetto Daniele Giaimo; Francesca Ferrante; Diana M Vallejo ; Kerstin Hein; Irene Gutierrez-Perez ...
 
 
Faithful chromosome segregation in Trypanosoma brucei requires a cohort of divergent spindle-associated proteins with distinct functions border= 
 
Qing Zhou; Kyu Joon Lee ; Yasuhiro Kurasawa; Huiqing Hu; Tai An ...
 
 
RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF border= 
 
Julian M Rozenberg ; Joan M Taylor; Christopher P Mack
 
 
A multivariate prediction model for Rho-dependent termination of transcription border=  
 
Cédric Nadiras; Eric Eveno; Annie Schwartz ; Nara Figueroa-Bossi; Marc Boudvillain
 
 
Rpd3L HDAC links H3K4me3 to transcriptional repression memory border= 
 
Bo Bae Lee; Ahyoung Choi; Ji Hyun Kim ; Yukyung Jun; Hyeonju Woo ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
Efficient CRISPR/Cas9-mediated editing of trinucleotide repeat expansion in myotonic dystrophy patient-derived iPS and myogenic cells border= 
 
Sumitava Dastidar ; Simon Ardui; Kshitiz Singh; Debanjana Majumdar; Nisha Nair ...
 
 
Germline DNA replication timing shapes mammalian genome composition border=  
 
Yishai Yehuda; Britny Blumenfeld; Nina Mayorek ; Kirill Makedonski; Oriya Vardi ...
 
 
ATR-mediated proteome remodeling is a major determinant of homologous recombination capacity in cancer cells border=  
 
Dongsung Kim; Yi Liu; Susannah Oberly ; Raimundo Freire; Marcus B Smolka
 
 
Combined deficiency of Senataxin and DNA-PKcs causes DNA damage accumulation and neurodegeneration in spinal muscular atrophy border= 
 
Annapoorna Kannan ; Kanchan Bhatia; Dana Branzei; Laxman Gangwani
 
 
The helicase Pif1 functions in the template switching pathway of DNA damage bypass border=  
 
Néstor García-Rodríguez; Ronald P Wong; Helle D Ulrich
 
 
The signature motif of the Saccharomyces cerevisiae Pif1 DNA helicase is essential in vivo for mitochondrial and nuclear functions and in vitro for ATPase activity border= 
 
Carly L Geronimo; Saurabh P Singh ; Roberto Galletto; Virginia A Zakian
 
 
 
Genomics
 
 
 
Shared nucleotide flanks confer transcriptional competency to bZip core motifs border=  
 
Daniel M Cohen; Hee-Woong Lim; Kyoung-Jae Won ; David J Steger
 
 
In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets border= 
 
Ben Niu; Denise M Coslo; Alain R Bataille; Istvan Albert; B Franklin Pugh ...
 
 
 
Molecular Biology
 
 
 
mRNAs are sorted for export or degradation before passing through nuclear speckles border= 
 
Jing Fan; Bin Kuai ; Ke Wang; Lantian Wang; Yimin Wang ...
 
 
Decoding non-random mutational signatures at Cas9 targeted sites border= 
 
Amir Taheri-Ghahfarokhi; Benjamin J M Taylor; Roberto Nitsch ; Anders Lundin; Anna-Lina Cavallo ...
 
 
MTG1 couples mitoribosome large subunit assembly with intersubunit bridge formation border=  
 
Hyun-Jung Kim; Antoni Barrientos
 
 
HIV-1 Vpr and p21 restrict LINE-1 mobility border= 
 
Koudai Kawano; Aurélien J Doucet; Mikinori Ueno ; Ryusho Kariya; Wenfeng An ...
 
 
The human Obg protein GTPBP10 is involved in mitoribosomal biogenesis border=  
 
Elena Lavdovskaia; Elisa Kolander; Emely Steube ; Mandy Mong-Quyen Mai; Henning Urlaub ...
 
 
 
Nucleic Acid Enzymes
 
 
 
Evolutionary insights into Trm112-methyltransferase holoenzymes involved in translation between archaea and eukaryotes border= 
 
Nhan van Tran ; Leslie Muller; Robert L Ross; Roxane Lestini; Juliette Létoquart ...
 
 
Single molecule kinetics uncover roles for E. coli RecQ DNA helicase domains and interaction with SSB border=  
 
Debjani Bagchi; Maria Manosas; Weiting Zhang ; Kelly A Manthei; Samar Hodeib ...
 
 
The Pif1 signature motif of Pfh1 is necessary for both protein displacement and helicase unwinding activities, but is dispensable for strand-annealing activity border= 
 
Jani B Mohammad ; Marcus Wallgren; Nasim Sabouri
 
 
Entropy-driven DNA logic circuits regulated by DNAzyme border= 
 
Jing Yang; Ranfeng Wu; Yifan Li ; Zhiyu Wang; Linqiang Pan ...
 
 
 
RNA and RNA-protein complexes
 
 
 
Structural accommodations accompanying splicing of a group II intron RNP border=  
 
Xiaolong Dong; Srivathsan Ranganathan; Guosheng Qu ; Carol Lyn Piazza; Marlene Belfort
 
 
SWI/SNF interacts with cleavage and polyadenylation factors and facilitates pre-mRNA 3² end processing border=  
 
Simei Yu; Antonio Jordán-Pla; Antoni Gañez-Zapater ; Shruti Jain; Anna Rolicka ...
 
 
Computational analysis of ribonomics datasets identifies long non-coding RNA targets of gamma -herpesviral miRNAs border=  
 
Sunantha Sethuraman; Merin Thomas; Lauren A Gay ; Rolf Renne
 
 
Structural insights into Drosophila -C3PO complex assembly and ˜Dynamic Side Port' model in substrate entry and release border= 
 
Xiaobing Mo; Xia Yang ; Yuren Adam Yuan
 
 
The essential nature of YqfG, a YbeY homologue required for 3² maturation of Bacillus subtilis 16S ribosomal RNA is suppressed by deletion of RNase R border= 
 
Kathrin Baumgardt; Laetitia Gilet ; Sabine Figaro; Ciarán Condon
 
 
 
Structural Biology
 
 
 
DNA binding with a minimal scaffold: structure'function analysis of Lig E DNA ligases border= 
 
Adele Williamson; Miriam Grgic ; Hanna-Kirsti S Leiros
 
 
Crystal structure of dimeric human PNPase reveals why disease-linked mutants suffer from low RNA import and degradation activities border= 
 
Bagher Golzarroshan ; Chia-Liang Lin; Chia-Lung Li; Wei-Zen Yang; Lee-Ya Chu ...
 
 
E. coli elongation factor Tu bound to a GTP analogue displays an open conformation equivalent to the GDP-bound form border= 
 
Jesper S Johansen; Darius Kavaliauskas; Shawn H Pfeil; Mickaël Blaise; Barry S Cooperman ...
 
 
Structural dynamics of translation elongation factor Tu during aa-tRNA delivery to the ribosome border=  
 
Darius Kavaliauskas; Chunlai Chen; Wei Liu ; Barry S Cooperman; Yale E Goldman ...
 
 
 
Corrigendum
 
 
 
RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF border= 
 
Julian M Rozenberg ; Joan M Taylor; Christopher P Mack
 
 
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 ...
 
 
Generating genomic platforms to study Candida albicans pathogenesis border=  
 
Mélanie Legrand; Sophie Bachellier-Bassi; Keunsook K Lee ; Yogesh Chaudhari; Hélène Tournu ...
 
 
 
Methods Online
 
 
 
SB Driver Analysis: a Sleeping Beauty cancer driver analysis framework for identifying and prioritizing experimentally actionable oncogenes and tumor suppressors border= 
 
Justin Y Newberg ; Michael A Black; Nancy A Jenkins; Neal G Copeland; Karen M Mann ...
 
 
Triazole linking for preparation of a next-generation sequencing library from single-stranded DNA border=  
 
Fumihito Miura; Tomoko Fujino; Kanako Kogashi ; Yukiko Shibata; Miki Miura ...
 
 
BASiNET'BiologicAl Sequences NETwork: a case study on coding and non-coding RNAs identification border=  
 
Eric Augusto Ito; Isaque Katahira; Fábio Fernandes da Rocha Vicente ; Luiz Filipe Protasio Pereira; Fabrício Martins Lopes
 
 
RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications border=  
 
Danny Incarnato; Edoardo Morandi; Lisa Marie Simon ; Salvatore Oliviero
 
 
Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA border=  
 
Daniel M Dayeh; William A Cantara; Jonathan P Kitzrow ; Karin Musier-Forsyth; Kotaro Nakanishi
 
 
A novel lambda integrase-mediated seamless vector transgenesis platform for therapeutic protein expression border=  
 
Harshyaa Makhija; Suki Roy; Shawn Hoon ; Farid John Ghadessy; Desmond Wong ...
 
 
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