Subject: Nucleic Acids Research Table of Contents for 10 January 2019 ------=_Part_774031594.1547399973118 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_774031594.1547399973118 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Nucleic Acids Research  
Volume 47 Issue 1
 
10 January 2019
 
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Editorial
 
 
 
Editorial: Preprints, citations and Nucleic Acids Research border=  
 
Barry L Stoddard; Keith R Fox
 
 
 
NAR Breakthrough Article
 
 
 
Inosine induces context-dependent recoding and translational stalling border=  
 
Konstantin Licht; Markus Hartl; Fabian Amman ; Dorothea Anrather; Michael P Janisiw ...
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Structure guided fluorescence labeling reveals a two-step binding mechanism of neomycin to its RNA aptamer border= 
 
Henrik Gustmann; Anna-Lena J Segler; Dnyaneshwar B Gophane; Andreas J Reuss; Christian Grünewald ...
 
 
Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study border=  
 
Ryota Yamagami; Mohammad Kayedkhordeh; David H Mathews ; Philip C Bevilacqua
 
 
Assaying RNA structure with LASER-Seq border= 
 
Boris Zinshteyn; Dalen Chan; Whitney England ; Chao Feng; Rachel Green ...
 
 
Binding of cellular nucleolin with the viral core RNA G-quadruplex structure suppresses HCV replication border= 
 
Wen-Xiu Bian; Yan Xie ; Xiao-Ning Wang; Guo-Hua Xu; Bo-Shi Fu ...
 
 
 
Computational Biology
 
 
 
Kinetic pathways of topology simplification by Type-II topoisomerases in knotted supercoiled DNA border= 
 
Riccardo Ziraldo; Andreas Hanke; Stephen D Levene
 
 
E. coli gene regulatory networks are inconsistent with gene expression data border=  
 
Simon J Larsen; Richard Röttger; Harald H H W Schmidt ; Jan Baumbach
 
 
Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design border= 
 
Jae Young Lee ; Young-Joo Kim; Chanseok Lee; Jae Gyung Lee; Hiromasa Yagyu ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Activation of the oncogenic transcription factor B-Myb via multisite phosphorylation and prolyl cis/trans isomerization border= 
 
Eugen Werwein; Hannah Cibis ; Daniel Hess; Karl-Heinz Klempnauer
 
 
Human SETMAR is a DNA sequence-specific histone-methylase with a broad effect on the transcriptome border=  
 
Michael Tellier; Ronald Chalmers
 
 
Resting cells rely on the DNA helicase component MCM2 to build cilia border=  
 
Teresa Casar Tena; Lars D Maerz; Karol Szafranski ; Marco Groth; Tamara J Blätte ...
 
 
DNMT3L facilitates DNA methylation partly by maintaining DNMT3A stability in mouse embryonic stem cells border=  
 
Nicolas Veland; Yue Lu; Swanand Hardikar ; Sally Gaddis; Yang Zeng ...
 
 
DOT1L promotes progenitor proliferation and primes neuronal layer identity in the developing cerebral cortex border=  
 
Henriette Franz; Alejandro Villarreal; Stefanie Heidrich ; Pavankumar Videm; Fabian Kilpert ...
 
 
Methylation of UHRF1 by SET7 is essential for DNA double-strand break repair border=  
 
Ja Young Hahm; Ji-Young Kim; Jin Woo Park ; Joo-Young Kang; Kee-Beom Kim ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
The RecB helicase-nuclease tether mediates Chi hotspot control of RecBCD enzyme border= 
 
Susan K Amundsen; Gerald R Smith
 
 
Single-molecule imaging of DNA gyrase activity in living Escherichia coli border=  
 
Mathew Stracy; Adam J M Wollman; Elzbieta Kaja ; Jacek Gapinski; Ji-Eun Lee ...
 
 
Genome-wide mapping of 8-oxo-7,8-dihydro-2²-deoxyguanosine reveals accumulation of oxidatively-generated damage at DNA replication origins within transcribed long genes of mammalian cells border= 
 
Stefano Amente ; Giacomo Di Palo; Giovanni Scala; Tiziana Castrignanò; Francesca Gorini ...
 
 
A genetic screen pinpoints ribonucleotide reductase residues that sustain dNTP homeostasis and specifies a highly mutagenic type of dNTP imbalance border= 
 
Tobias T Schmidt ; Sushma Sharma; Gloria X Reyes; Kerstin Gries; Maike Gross ...
 
 
 
Molecular Biology
 
 
 
BREX system of Escherichia coli distinguishes self from non-self by methylation of a specific DNA site border= 
 
Julia Gordeeva; Natalya Morozova ; Nicolas Sierro; Artem Isaev; Tomas Sinkunas ...
 
 
Trypanosomes can initiate nuclear export co-transcriptionally border= 
 
Carina Goos; Mario Dejung; Ann M Wehman ; Elisabeth M-Natus; Johannes Schmidt ...
 
 
Telomere shortening by transgenerational transmission of TNF-alpha -induced TERRA via ATF7 border=  
 
Binbin Liu; Toshio Maekawa; Keisuke Yoshida ; Nhung Hong Ly; Kimiko Inoue ...
 
 
 
Nucleic Acid Enzymes
 
 
 
A dual-functional priming-capping loop of rhabdoviral RNA polymerases directs terminal de novo initiation and capping intermediate formation border= 
 
Minako Ogino; Nirmala Gupta ; Todd J Green; Tomoaki Ogino
 
 
RNA polymerase III subunits C37/53 modulate rU:dA hybrid 3² end dynamics during transcription termination 
 
Saurabh Mishra; Richard J Maraia
 
 
 
RNA and RNA-protein complexes
 
 
 
A combinatorial code for mRNA 3²-UTR-mediated translational control in the mouse oocyte border= 
 
Xing-Xing Dai; Jun-Chao Jiang ; Qian-Qian Sha; Yu Jiang; Xiang-Hong Ou ...
 
 
TDP-43 enhances translation of specific mRNAs linked to neurodegenerative disease border=  
 
Nagammal Neelagandan; Giorgio Gonnella; Stefan Dang ; Philipp C Janiesch; Katharine K Miller ...
 
 
N6-methyladenosine modification and METTL3 modulate enterovirus 71 replication border=  
 
Haojie Hao; Sujuan Hao; Honghe Chen ; Zhen Chen; Yanfang Zhang ...
 
 
IGF2BP1 promotes SRF-dependent transcription in cancer in a m6A- and miRNA-dependent manner border=  
 
Simon Müller; Markus Glaß; Anurag K Singh ; Jacob Haase; Nadine Bley ...
 
 
TOE1 acts as a 3² exonuclease for telomerase RNA and regulates telomere maintenance border=  
 
Tingting Deng; Yan Huang; Kai Weng ; Song Lin; Yujing Li ...
 
 
Ribosomal protein eL24, involved in two intersubunit bridges, stimulates translation initiation and elongation border=  
 
Ivan Kisly; Jaanus Remme; Tiina Tamm
 
 
Alu insertion variants alter mRNA splicing border= 
 
Lindsay M Payer; Jared P Steranka; Daniel Ardeljan ; JaNiece Walker; Kathryn C Fitzgerald ...
 
 
Dom34 mediates targeting of exogenous RNA in the antiviral OAS/RNase L pathway border=  
 
Takuto Nogimori; Kyutatsu Nishiura; Sho Kawashima ; Takahiro Nagai; Yuka Oishi ...
 
 
 
Structural Biology
 
 
 
Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI border= 
 
Betty W Shen; Lindsey Doyle; Phil Bradley; Daniel F Heiter; Keith D Lunnen ...
 
 
Structural analysis of fungal CENP-H/I/K homologs reveals a conserved assembly mechanism underlying proper chromosome alignment border= 
 
Liqiao Hu ; Hao Huang; Mohan Hei; Yang Yang; Sheng Li ...
 
 
Deducing putative ancestral forms of GNRA/receptor interactions from the ribosome border=  
 
Erin R Calkins; Paul Zakrevsky; Vasken L Keleshian ; Eduardo G Aguilar; Cody Geary ...
 
 
Structural insights into a unique preference for 3² terminal guanine of mirtron in Drosophila TUTase tailor border=  
 
Lin Cheng; Fudong Li; Yiyang Jiang ; Hailong Yu; Changlin Xie ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
A tightly regulated and adjustable CRISPR-dCas9 based AND gate in yeast border=  
 
Anja Hofmann; Johannes Falk; Tim Prangemeier ; Dominic Happel; Adrian Köber ...
 
 
 
Methods Online
 
 
 
CRISPR-Cap: multiplexed double-stranded DNA enrichment based on the CRISPR system border= 
 
Jeewon Lee; Hyeonseob Lim ; Hoon Jang; Byungjin Hwang; Joon Ho Lee ...
 
 
De novo clustering of long reads by gene from transcriptomics data border=  
 
Camille Marchet; Lolita Lecompte; Corinne Da Silva ; Corinne Cruaud; Jean-Marc Aury ...
 
 
ProGeM: a framework for the prioritization of candidate causal genes at molecular quantitative trait loci border=  
 
David Stacey; Eric B Fauman; Daniel Ziemek ; Benjamin B Sun; Eric L Harshfield ...
 
 
Targeting individual cells by barcode in pooled sequence libraries border=  
 
Navpreet Ranu; Alexandra-Chloé Villani; Nir Hacohen ; Paul C Blainey
 
 
Ribose-Map: a bioinformatics toolkit to map ribonucleotides embedded in genomic DNA border=  
 
Alli L Gombolay; Fredrik O Vannberg; Francesca Storici
 
 
Detection of epigenetic field defects using a weighted epigenetic distance-based method border=  
 
Ya Wang; Min Qian; Peifeng Ruan ; Andrew E Teschendorff; Shuang Wang
 
 
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