Subject: Nucleic Acids Research Table of Contents for 27 July 2018 ------=_Part_422380693.1532887759404 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_422380693.1532887759404 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Nucleic Acids Research  
Volume 46 Issue 13
 
27 July 2018
 
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NAR Breakthrough Article
 
 
 
Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription border= 
 
Ivan A Belashov; David W Crawford; Chapin E Cavender ; Peng Dai; Patrick C Beardslee ...
 
 
Survey and Summary
 
 
 
A survey of recent unusual high-resolution DNA structures provoked by mismatches, repeats and ligand binding border= 
 
Roshan Satange; Chung-ke Chang; Ming-Hon Hou
 
 
How to create state-of-the-art genetic model systems: strategies for optimal CRISPR-mediated genome editing border= 
 
Yannik Bollen; Jasmin Post; Bon-Kyoung Koo ; Hugo J G Snippert
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
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 ...
 
 
HgII binds to C'T mismatches with high affinity border= 
 
Olivia P Schmidt; Andrea S Benz ; Guillaume Mata; Nathan W Luedtke
 
 
Computational Biology
 
 
 
Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant border= 
 
Jonas Defoort; Yves Van de Peer; Vanessa Vermeirssen
 
 
Transfer-matrix calculations of the effects of tension and torque constraints on DNA'protein interactions border=  
 
Artem K Efremov; Jie Yan
 
 
An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch border= 
 
Miroslav Krepl ; Jennifer Vögele; Holger Kruse; Elke Duchardt-Ferner; Jens Wöhnert ...
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Cyclin-dependent kinase 1 activity coordinates the chromatin associated state of Oct4 during cell cycle in embryonic stem cells border= 
 
Hye Ji Kim ; Jihoon Shin; Sangho Lee; Tae Wan Kim; Hyonchol Jang ...
 
 
The polyadenosine RNA-binding protein ZC3H14 interacts with the THO complex and coordinately regulates the processing of neuronal transcripts border= 
 
Kevin J Morris ; Anita H Corbett
 
 
Methylation of hypoxia-inducible factor (HIF)-1alpha by G9a/GLP inhibits HIF-1 transcriptional activity and cell migration border= 
 
Lei Bao; Yan Chen; Hsien-Tsung Lai; Shwu-Yuan Wu; Jennifer E Wang ...
 
 
Zinc finger proteins orchestrate active gene silencing during embryonic stem cell differentiation border= 
 
Sojung Kwak ; Tae Wan Kim; Byung-Hee Kang; Jae-Hwan Kim; Jang-Seok Lee ...
 
 
PHD finger protein 1 (PHF1) is a novel reader for histone H4R3 symmetric dimethylation and coordinates with PRMT5'WDR77/CRL4B complex to promote tumorigenesis border= 
 
Ruiqiong Liu ; Jie Gao; Yang Yang; Rongfang Qiu; Yu Zheng ...
 
 
Genome Integrity, Repair and Replication
 
 
 
The archaeal ATPase PINA interacts with the helicase Hjm via its carboxyl terminal KH domain remodeling and processing replication fork and Holliday junction border= 
 
Binyuan Zhai ; Kevin DuPrez; Xiaoyun Han; Zenglin Yuan; Sohail Ahmad ...
 
 
Base-excision repair deficiency alone or combined with increased oxidative stress does not increase mtDNA point mutations in mice border= 
 
Johanna H K Kauppila ; Nina A Bonekamp; Arnaud Mourier; Marita A Isokallio; Alexandra Just ...
 
 
RecBCD coordinates repair of two ends at a DNA double-strand break, preventing aberrant chromosome amplification border= 
 
Martin A White; Benura Azeroglu; Manuel A Lopez-Vernaza; A M Mahedi Hasan; David R F Leach
 
 
Genome-wide analysis of the spatiotemporal regulation of firing and dormant replication origins in human cells border=  
 
Nozomi Sugimoto; Kazumitsu Maehara; Kazumasa Yoshida ; Yasuyuki Ohkawa; Masatoshi Fujita
 
 
An Orc1/Cdc6 ortholog functions as a key regulator in the DNA damage response in Archaea border= 
 
Mengmeng Sun; Xu Feng; Zhenzhen Liu; Wenyuan Han ; Yun Xiang Liang ...
 
 
Genomics
 
 
 
Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing 
 
Jung-Hyun Kim; Alexander T Dilthey; Ramaiah Nagaraja; Hee-Sheung Lee; Sergey Koren ...
 
 
Molecular Biology
 
 
 
Multifactorial control of the expression of a CRISPR-Cas system by an extracytoplasmic function σ/anti-σ pair and a global regulatory complex border= 
 
Diego Bernal-Bernal; Javier Abellón-Ruiz; Antonio A Iniesta; Elena Pajares-Martínez ; Eva Bastida-Martínez ...
 
 
sRNA-dependent control of curli biosynthesis in Escherichia coli: McaS directs endonucleolytic cleavage of csgD mRNA border= 
 
Patrick Rosendahl Andreassen; Jens Sivkær Pettersen; Mateusz Szczerba; Poul Valentin-Hansen; Jakob Møller-Jensen ...
 
 
Nucleic Acid Enzymes
 
 
 
Coulomb and CH'euro  interactions in (6'4) photolyase'DNA complex dominate DNA binding and repair abilities border= 
 
Yuma Terai; Ryuma Sato; Takahiro Yumiba; Ryuhei Harada; Kohei Shimizu ...
 
 
Gyrase containing a single C-terminal domain catalyzes negative supercoiling of DNA by decreasing the linking number in steps of two border=  
 
Jampa Tsedön Stelljes; Daniela Weidlich; Airat Gubaev ; Dagmar Klostermeier
 
 
Mechanism for de novo initiation at two sites in the respiratory syncytial virus promoter border= 
 
Tessa N Cressey; Sarah L Noton; Kartikeya Nagendra; Molly R Braun; Rachel Fearns
 
 
RNA and RNA-protein complexes
 
 
 
High-resolution RNA 3-ends mapping of bacterial Rho-dependent transcripts border= 
 
Daniel Dar; Rotem Sorek
 
 
Differences in silencing of mismatched targets by sliced versus diced siRNAs border= 
 
Guihua Sun ; Jinghan Wang; Yasheng Huang; Christine Wan-Yin Yuan; Keqiang Zhang ...
 
 
Genome-wide mapping of the RNA targets of the Pseudomonas aeruginosa riboregulatory protein RsmN border= 
 
Manuel Romero; Hazel Silistre ; Laura Lovelock; Victoria J Wright; Kok-Gan Chan ...
 
 
Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF border= 
 
Ang Gao; Nikita Vasilyev; Daniel J Luciano ; Rose Levenson-Palmer; Jamie Richards ...
 
 
In vitro reconstitution and analysis of eukaryotic RNase P RNPs border= 
 
Anna Perederina; Igor Berezin; Andrey S Krasilnikov
 
 
Structural Biology
 
 
 
Structure and ligand binding of the SAM-V riboswitch border= 
 
Lin Huang; David M J Lilley
 
 
DapF stabilizes the substrate-favoring conformation of RppH to stimulate its RNA-pyrophosphohydrolase activity in Escherichia coli border=  
 
Qiang Wang; Delin Zhang; Zeyuan Guan ; Dongqin Li; Kai Pei ...
 
 
Structural motifs in eIF4G and 4E-BPs modulate their binding to eIF4E to regulate translation initiation in yeast border= 
 
Stefan Grüner; Ramona Weber; Daniel Peter; Min-Yi Chung ; Cátia Igreja ...
 
 
Synthetic Biology and Bioengineering
 
 
 
Intron-containing algal transgenes mediate efficient recombinant gene expression in the green microalga Chlamydomonas reinhardtii border= 
 
Thomas Baier; Julian Wichmann; Olaf Kruse; Kyle J Lauersen
 
 
A functional type II-A CRISPR'Cas system from Listeria enables efficient genome editing of large non-integrating bacteriophage border= 
 
Mario Hupfeld; Despoina Trasanidou ; Livia Ramazzini; Jochen Klumpp; Martin J Loessner ...
 
 
Methods Online
 
 
 
Circular permutation profiling by deep sequencing libraries created using transposon mutagenesis border= 
 
Joshua T Atkinson; Alicia M Jones; Quan Zhou; Jonathan J Silberg
 
 
Formation of correlated chromatin domains at nanoscale dynamic resolution during transcription border= 
 
Haitham A Shaban ; Roman Barth; Kerstin Bystricky
 
 
High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing border= 
 
Alexandra M de Paz; Thaddeus R Cybulski; Adam H Marblestone; Bradley M Zamft ; George M Church ...
 
 
A single-molecule sequencing assay for the comprehensive profiling of T4 DNA ligase fidelity and bias during DNA end-joining border= 
 
Vladimir Potapov; Jennifer L Ong; Bradley W Langhorst; Katharina Bilotti; Dan Cahoon ...
 
 
A CRISPR/molecular beacon hybrid system for live-cell genomic imaging border= 
 
Xiaotian Wu ; Shiqi Mao; Yantao Yang; Muaz N Rushdi; Christopher J Krueger ...
 
 
Introducing structure-switching functionality into small-molecule-binding aptamers via nuclease-directed truncation border= 
 
Zongwen Wang; Haixiang Yu; Juan Canoura; Yingzhu Liu; Obtin Alkhamis ...
 
 
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