Subject: Nucleic Acids Research Table of Contents for 29 September 2017 Oxford Academic
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Nucleic Acids Research  
Volume 45 Issue 17
29 September 2017
Chemical Biology and Nucleic Acid Chemistry
Self-biotinylation of DNA G-quadruplexes via intrinsic peroxidase activity border= 
Owen J. Einarson; Dipankar Sen
Computational Biology
Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation border= 
Yu Zhang; Ross C. Hardison
Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture border= 
Maria Bouvy-Liivrand ; Ana Hernández de Sande; Petri Pölönen; Juha Mehtonen; Tapio Vuorenmaa ...
Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S. pombe  border= 
Fabrizio Benedetti; Dusan Racko ; Julien Dorier; Yannis Burnier; Andrzej Stasiak
Data Resources and Analyses
Meta-analysis of transcriptomic datasets identifies genes enriched in the mammalian circadian pacemaker border= 
Laurence A. Brown; John Williams ; Lewis Taylor; Ross J. Thomson; Patrick M. Nolan ...
Gene Regulation, Chromatin and Epigenetics
LMO2 is required for TAL1 DNA binding activity and initiation of definitive haematopoiesis at the haemangioblast stage border= 
Vesna S. Stanulović; Pierre Cauchy; Salam A. Assi; Maarten Hoogenkamp
p53 regulates enhancer accessibility and activity in response to DNA damage border= 
Scott T. Younger; John L. Rinn
dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression border= 
Henriette O'Geen ; Chonghua Ren; Charles M. Nicolet; Andrew A. Perez; Julian Halmai ...
HMGN1 and 2 remodel core and linker histone tail domains within chromatin border= 
Kevin J. Murphy; Amber R. Cutter ; He Fang; Yuri V. Postnikov; Michael Bustin ...
Dual function of Swc5 in SWR remodeling ATPase activation and histone H2A eviction border= 
Lu Sun; Ed Luk
Quantitative proteomics reveals that long non-coding RNA MALAT1 interacts with DBC1 to regulate p53 acetylation border= 
Ruibing Chen ; Yun Liu; Hao Zhuang; Baicai Yang; Kaiwen Hei ...
MAZ induces MYB expression during the exit from quiescence via the E2F site in the MYB promoter border= 
Josué à lvaro-Blanco; Katia Urso ; Yuri Chiodo; Carla Martín-Cortázar; Omar Kourani ...
Salmonella STM1697 coordinates flagella biogenesis and virulence by restricting flagellar master protein FlhD4C2 from recruiting RNA polymerase border=  
Bingqing Li; Yingying Yue; Zenglin Yuan ; Fengyu Zhang; Peng Li ...
A transcription network of interlocking positive feedback loops maintains intracellular iron balance in archaea border= 
Mar Martinez-Pastor; W. Andrew Lancaster; Peter D. Tonner; Michael W. W. Adams ; Amy K. Schmid
TET2- and TDG-mediated changes are required for the acquisition of distinct histone modifications in divergent terminal differentiation of myeloid cells border= 
Antonio Garcia-Gomez; Tianlu Li; Martin Kerick; Francesc CatalĂ -Moll; Natalia R. Comet ...
Genome Integrity, Repair and Replication
Polmu tumor variants decrease the efficiency and accuracy of NHEJ border= 
Guillermo Sastre-Moreno ; John M. Pryor; Alberto Díaz-Talavera; José F. Ruiz; Dale A. Ramsden ...
Parallel triplex structure formed between stretched single-stranded DNA and homologous duplex DNA border= 
Jin Chen; Qingnan Tang ; Shiwen Guo; Chen Lu; Shimin Le ...
Modulation of proteostasis counteracts oxidative stress and affects DNA base excision repair capacity in ATM-deficient cells border= 
Mattia Poletto; Di Yang; Sally C. Fletcher ; Iolanda Vendrell; Roman Fischer ...
Redundancy between nucleases required for homologous recombination promotes PARP inhibitor resistance in the eukaryotic model organism Dictyostelium border= 
Anna-Lena Kolb; Alasdair R. Gunn; Nicholas D. Lakin
MutSbeta abundance and Msh3 ATP hydrolysis activity are important drivers of CTG˘CAG repeat expansions border= 
Norma Keogh; Kara Y. Chan ; Guo-Min Li; Robert S. Lahue
Complementation of aprataxin deficiency by base excision repair enzymes in mitochondrial extracts border= 
Melike Çağlayan; Rajendra Prasad; Rachel Krasich; Matthew J. Longley ; Kei Kadoda ...
The abundance of Fob1 modulates the efficiency of rRFBs to stall replication forks border= 
Alicia Castán; Pablo Hernández; Dora B. Krimer; Jorge B. Schvartzman
Mechanisms of transcription factor-mediated direct reprogramming of mouse embryonic stem cells to trophoblast stem-like cells border= 
Catherine Rhee; Bum-Kyu Lee; Samuel Beck; Lucy LeBlanc; Haley O. Tucker ...
Molecular Biology
Distinct roles of Pcf11 zinc-binding domains in pre-mRNA 3˛-end processing border=  
Julia Guéguéniat; Adrien F. Dupin; Johan Stojko ; Lionel Beaurepaire; Sarah Cianférani ...
Coexistence of two main folded G-quadruplexes within a single G-rich domain in the EGFR promoter border= 
Maria L. Greco; Anita Kotar; Riccardo Rigo; Camilla Cristofari ; Janez Plavec ...
Stimulation of reverse transcriptase generated cDNAs with specific indels by template RNA structure: retrotransposon, dNTP balance, RT-reagent usage border= 
Christophe Penno; Romika Kumari; Pavel V. Baranov; Douwe van Sinderen; John F. Atkins
Specific reverse transcriptase slippage at the HIV ribosomal frameshift sequence: potential implications for modulation of GagPol synthesis border= 
Christophe Penno; Romika Kumari; Pavel V. Baranov; Douwe van Sinderen; John F. Atkins
The kinetic mechanism of bacterial ribosome recycling border= 
Yuanwei Chen; Akira Kaji ; Hideko Kaji; Barry S. Cooperman
Nucleic Acid Enzymes
Mechanism of opening a sliding clamp border= 
Lauren G. Douma; Kevin K. Yu; Jennifer K. England; Marcia Levitus ; Linda B. Bloom
Pausing kinetics dominates strand-displacement polymerization by reverse transcriptase border= 
Omri Malik; Hadeel Khamis; Sergei Rudnizky; Ailie Marx; Ariel Kaplan
RNA and RNA-protein complexes
Interplay between PTB and miR-1285 at the p53 3˛UTR modulates the levels of p53 and its isoform Î'40p53alpha  border= 
Aanchal Katoch ; Biju George; Amrutha Iyyappan; Debjit Khan; Saumitra Das
Preferential microRNA targeting revealed by in vivo competitive binding and differential Argonaute immunoprecipitation border= 
Stanislas Werfel; Simon Leierseder ; Benjamin Ruprecht; Bernhard Kuster; Stefan Engelhardt
ARS2 is a general suppressor of pervasive transcription border= 
Claudia Iasillo; Manfred Schmid; Yousra Yahia; Muhammad A. Maqbool ; Nicolas Descostes ...
Direct modulation of T-box riboswitch-controlled transcription by protein synthesis inhibitors border= 
Vassiliki Stamatopoulou; Maria Apostolidi; Shuang Li; Katerina Lamprinou; Athanasios Papakyriakou ...
An RNA-targeted therapy for dystrophic epidermolysis bullosa border= 
Patricia Peking ; Ulrich Koller; Blanca Duarte; Rodolfo Murillas; Susanne Wolf ...
Structural Biology
Decomposing protein'DNA binding and recognition using simplified protein models border= 
LoĂŻc Etheve; Juliette Martin ; Richard Lavery
Structural insights of lincosamides targeting the ribosome of Staphylococcus aureus border= 
Donna Matzov; Zohar Eyal; Raphael I. Benhamou; Moran Shalev-Benami; Yehuda Halfon ...
The structure of transcription termination factor Nrd1 reveals an original mode for GUAA recognition border= 
Elsa Franco-Echevarría ; Noelia González-Polo; Silvia Zorrilla; Santiago Martínez-Lumbreras; Clara M. Santiveri ...
Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs border= 
Karolina Michalska; Grant C. Gucinski; Fernando Garza-Sánchez; Parker M. Johnson; Lucy M. Stols ...
Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA border=  
William Copp; Alexey Y. Denisov; Jingwei Xie ; Anne M. Noronha; Christopher Liczner ...
Methods Online
Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps border= 
Rajendra Kumar; Haitham Sobhy; Per Stenberg; Ludvig Lizana
Targeted chromatin ligation, a robust epigenetic profiling technique for small cell numbers border= 
Mark A. Zarnegar; Felicia Reinitz ; Aaron M. Newman; Michael F. Clarke
Expression of short hairpin RNAs using the compact architecture of retroviral microRNA genes border= 
James M. Burke; Rodney P. Kincaid; Francesca Aloisio; Nicole Welch ; Christopher S. Sullivan
paraGSEA: a scalable approach for large-scale gene expression profiling border= 
Shaoliang Peng; Shunyun Yang; Xiaochen Bo; Fei Li
Using neural networks for reducing the dimensions of single-cell RNA-Seq data border= 
Chieh Lin; Siddhartha Jain ; Hannah Kim; Ziv Bar-Joseph
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