Subject: Nucleic Acids Research Table of Contents for 10 October 2019 ------=_Part_713236605.1569951617274 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_713236605.1569951617274 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Nucleic Acids Research  
Volume 47 Issue 18
 
10 October 2019
 
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A CRISPR-Cas9 screen identifies essential CTCF anchor sites for estrogen receptor-driven breast cancer cell proliferation border= 
 
Gozde Korkmaz ; Zohar Manber; Rui Lopes; Stefan Prekovic; Karianne Schuurman ...
 
 
 
 
Circularization of flavivirus genomic RNA inhibits de novo translation initiation border= 
 
Thomas J Sanford; Harriet V Mears ; Teodoro Fajardo, Jr; Nicolas Locker; Trevor R Sweeney
 
 
 
 
AGO-unbound cytosolic pool of mature miRNAs in plant cells reveals a novel regulatory step at AGO1 loading border= 
 
Ágnes Dalmadi ; Péter Gyula; Jeannette Bálint; György Szittya; Zoltán Havelda
 
 
 
 
Remodeling of the Caenorhabditis elegans non-coding RNA transcriptome by heat shock border= 
 
William P Schreiner; Delaney C Pagliuso; Jacob M Garrigues; Jerry S Chen; Antti P Aalto ...
 
 
 
 
ATP/ADP modulates gp16'pRNA conformational change in the Phi29 DNA packaging motor border= 
 
Rujie Cai ; Ian R Price; Fang Ding; Feifei Wu; Ting Chen ...
 
 
 
 
Specificity of MYB interactions relies on motifs in ordered and disordered contexts border= 
 
Peter S Millard ; Konrad Weber; Birthe B Kragelund; Meike Burow
 
 
 
 
AT-dinucleotide rich sequences drive fragile site formation border= 
 
Michal Irony-Tur Sinai ; Anita Salamon; Noemie Stanleigh; Tchelet Goldberg; Aryeh Weiss ...
 
 
 
 
PPARbeta /delta recruits NCOR and regulates transcription reinitiation of ANGPTL4  border= 
 
Nathalie Legrand; Clemens L Bretscher ; Svenja Zielke; Bernhard Wilke; Michael Daude ...
 
 
 
NAR Breakthrough Article
 
 
 
DNA-PKcs promotes chromatin decondensation to facilitate initiation of the DNA damage response border= 
 
Huiming Lu ; Janapriya Saha; Pauline J Beckmann; Eric A Hendrickson; Anthony J Davis
 
 
 
Survey and Summary
 
 
 
Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function border= 
 
Christina E Weinberg ; Zasha Weinberg; Christian Hammann
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Polymerase synthesis of four-base DNA from two stable dimeric nucleotides border= 
 
Michael G Mohsen ; Debin Ji; Eric T Kool
 
 
Exploration of intramolecular split G-quadruplex and its analytical applications border= 
 
Mengmeng Lv ; Yuchun Guo; Jiangtao Ren; Erkang Wang
 
 
 
Computational Biology
 
 
 
Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning border= 
 
Diana Buitrago ; Laia Codó; Ricard Illa; Pau de Jorge; Federica Battistini ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
The mRNA degradation factor Xrn1 regulates transcription elongation in parallel to Ccr4 border= 
 
Victoria Begley ; Daniel Corzo; Antonio Jordán-Pla; Abel Cuevas-Bermúdez; Lola de Miguel-Jiménez ...
 
 
Transcriptome analyses of cells carrying the Type II Csp231I restriction'modification system reveal cross-talk between two unrelated transcription factors: C protein and the Rac prophage repressor border= 
 
Alessandro Negri ; Marcin JÄ.kalski; Aleksandra Szczuka; Leszek P Pryszcz; Iwona Mruk
 
 
Enhancement of LacI binding in vivo border=  
 
Manyu Du; Seth Kodner; Lu Bai
 
 
EWS'FLI1 modulated alternative splicing of ARID1A reveals novel oncogenic function through the BAF complex border= 
 
Saravana P Selvanathan ; Garrett T Graham; Alexander R Grego; Tabari M Baker; J Robert Hogg ...
 
 
Antagonistic and synergistic epigenetic modulation using orthologous CRISPR/dCas9-based modular system border= 
 
Goran Josipović ; Vanja Tadić; Marija Klasić; Vladimir Zanki; Ivona Bečeheli ...
 
 
The autoregulator Aca2 mediates anti-CRISPR repression border=  
 
Nils Birkholz; Robert D Fagerlund; Leah M Smith; Simon A Jackson; Peter C Fineran
 
 
 
Genome Integrity, Repair and Replication
 
 
 
Repair of base damage within break-induced replication intermediates promotes kataegis associated with chromosome rearrangements border= 
 
Rajula Elango; Beth Osia ; Victoria Harcy; Ewa Malc; Piotr A Mieczkowski ...
 
 
Dynamic architecture of the Escherichia coli structural maintenance of chromosomes (SMC) complex, MukBEF border= 
 
Karthik V Rajasekar ; Rachel Baker; Gemma L M Fisher; Jani R Bolla; Jarno Mäkelä ...
 
 
Molecular characteristics of reiterative DNA unwinding by the Caenorhabditis elegans RecQ helicase border= 
 
Seoyun Choi; Seung-Won Lee ; Hajin Kim; Byungchan Ahn
 
 
USP11 acts as a histone deubiquitinase functioning in chromatin reorganization during DNA repair border= 
 
Xia Ting ; Lu Xia; Jianguo Yang; Lin He; Wenzhe Si ...
 
 
 
Genomics
 
 
 
Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA border= 
 
V Talya Yerlici ; Michael W Lu; Carla R Hoge; Richard V Miller; Rafik Neme ...
 
 
 
Nucleic Acid Enzymes
 
 
 
A protein architecture guided screen for modification dependent restriction endonucleases border= 
 
Thomas Lutz ; Kiersten Flodman; Alyssa Copelas; Honorata Czapinska; Megumu Mabuchi ...
 
 
Stereospecificity control in aminoacyl-tRNA-synthetases: new evidence of d -amino acids activation and editing border= 
 
Mariia Yu Rybak; Alexey V Rayevsky ; Olga I Gudzera; Michael A Tukalo
 
 
 
RNA and RNA-protein complexes
 
 
 
Telomerase RNAs in land plants border= 
 
Petr Fajkus; Vratislav PeÅ¡ka ; Michal Závodník; Miloslava Fojtová; Jana Fulnečková ...
 
 
Insights into the base-pairing preferences of 8-oxoguanosine on the ribosome border= 
 
Erica N Thomas ; Carrie L Simms; Hannah E Keedy; Hani S Zaher
 
 
RsaC sRNA modulates the oxidative stress response of Staphylococcus aureus during manganese starvation border= 
 
David Lalaouna; Jessica Baude ; Zongfu Wu; Arnaud Tomasini; Johana Chicher ...
 
 
Regulation of La/SSB-dependent viral gene expression by pre-tRNA 3² trailer-derived tRNA fragments border= 
 
Hee Cho ; Wooseong Lee; Geon-Woo Kim; Seung-Hoon Lee; Jae-Su Moon ...
 
 
 
Structural Biology
 
 
 
Modelling and DNA topology of compact 2-start and 1-start chromatin fibres border= 
 
Chenyi Wu ; Andrew Travers
 
 
Structure and DNA damage-dependent derepression mechanism for the XRE family member DG-DdrO border= 
 
Huizhi Lu ; Liangyan Wang; Shengjie Li; Chaoming Pan; Kaiying Cheng ...
 
 
Structural and functional insight into the Mycobacterium tuberculosis protein PrpR reveals a novel type of transcription factor border= 
 
Su Tang; Nathan D Hicks; Yu-Shan Cheng; Andres Silva; Sarah M Fortune ...
 
 
Insights into telomeric G-quadruplex DNA recognition by HMGB1 protein border= 
 
Jussara Amato ; Linda Cerofolini; Diego Brancaccio; Stefano Giuntini; Nunzia Iaccarino ...
 
 
 
Methods Online
 
 
 
High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution border= 
 
Benjamin J Callahan ; Joan Wong; Cheryl Heiner; Steve Oh; Casey M Theriot ...
 
 
Long-read amplicon denoising border=  
 
Venkatesh Kumar; Thomas Vollbrecht; Mark Chernyshev; Sanjay Mohan; Brian Hanst ...
 
 
Nonparametric expression analysis using inferential replicate counts border= 
 
Anqi Zhu ; Avi Srivastava; Joseph G Ibrahim; Rob Patro; Michael I Love
 
 
A ˜poly-transfection' method for rapid, one-pot characterization and optimization of genetic systems border= 
 
Jeremy J Gam ; Breanna DiAndreth; Ross D Jones; Jin Huh; Ron Weiss
 
 
DNA skybridge: 3D structure producing a light sheet for high-throughput single-molecule imaging border= 
 
Daehyung Kim ; Fahad Rashid; Yeonmo Cho; Manal S Zaher; I I Hwan Cho ...
 
 
Infrared nanospectroscopic mapping of a single metaphase chromosome border= 
 
Ewelina Lipiec ; Francesco S Ruggeri; Carine Benadiba; Anna M Borkowska; Jan D Kobierski ...
 
 
Cytoplasmic DNA can be detected by RNA fluorescence in situ hybridization border= 
 
Eliraz Greenberg; Hodaya Hochberg-Laufer ; Shalev Blanga; Noa Kinor; Yaron Shav-Tal
 
 
A deep learning genome-mining strategy for biosynthetic gene cluster prediction border= 
 
Geoffrey D Hannigan ; David Prihoda; Andrej Palicka; Jindrich Soukup; Ondrej Klempir ...
 
 
LTMG: a novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data border= 
 
Changlin Wan ; Wennan Chang; Yu Zhang; Fenil Shah; Xiaoyu Lu ...
 
 
Genome-wide epistasis and co-selection study using mutual information border= 
 
Johan Pensar ; Santeri Puranen; Brian Arnold; Neil MacAlasdair; Juri Kuronen ...
 
 
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