Subject: Nucleic Acids Research Table of Contents for 29 September 2017 Oxford Academic
 
 
 
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New issue alert
 
Nucleic Acids Research  
Volume 45 Issue 17
 
29 September 2017
 
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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
 
 
Genomics
 
 
 
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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