Subject: Nucleic Acids Research Table of Contents for 4 May 2018 Oxford Academic
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Nucleic Acids Research  
Volume 46 Issue 8
4 May 2018
NAR Breakthrough Article
Extensive and systematic rewiring of histone post-translational modifications in cancer model systems border= 
Roberta Noberini; Daniela Osti; Claudia Miccolo; Cristina Richichi ; Michela Lupia ...
Survey and Summary
Structural dynamics of the N-terminal domain and the Switch loop of Prp8 during spliceosome assembly and activation border= 
Xu Jia; Chengfu Sun
Computational Biology
Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families border= 
Vladimir Reinharz; Antoine Soulé; Eric Westhof; Jérôme Waldispühl ; Alain Denise
FoldX accurate structural protein'DNA binding prediction using PADA1 (Protein Assisted DNA Assembly 1) border= 
Javier Delgado Blanco; Leandro Radusky; Héctor Climente-González; Luis Serrano
Gene Regulation, Chromatin and Epigenetics
Role for first zinc finger of WT1 in DNA sequence specificity: Denys'Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites border= 
Dongxue Wang; John R Horton; Yu Zheng; Robert M Blumenthal; Xing Zhang ...
PERK/eIF2alpha signaling inhibits HIF-induced gene expression during the unfolded protein response via YB1-dependent regulation of HIF1alpha translation border= 
Iglika G Ivanova ; Catherine V Park; Adrian I Yemm; Niall S Kenneth
Human CHD1 is required for early DNA-damage signaling and is uniquely regulated by its N terminus border= 
Jia Zhou; Jiaqi Li; Rodolfo B Serafim; Steven Ketchum; Catarina G Ferreira ...
N6-Methyladenosine modification of lincRNA 1281 is critically required for mESC differentiation potential border= 
Dandan Yang; Jing Qiao; Guiying Wang; Yuanyuan Lan; Guoping Li ...
Single-target regulators form a minor group of transcription factors in Escherichia coli K-12 border= 
Tomohiro Shimada ; Hiroshi Ogasawara; Akira Ishihama
High-resolution 3D models of Caulobacter crescentus chromosome reveal genome structural variability and organization border= 
Asli Yildirim; Michael Feig
Hierarchical interactions between Fnr orthologs allows fine-tuning of transcription in response to oxygen in Herbaspirillum seropedicae border= 
Marcelo Bueno Batista; Govind Chandra; Rose Adele Monteiro; Emanuel Maltempi de Souza ; Ray Dixon
Genome Integrity, Repair and Replication
Human RAD51 rapidly forms intrinsically dynamic nucleoprotein filaments modulated by nucleotide binding state border= 
Mário Å pírek; Jarmila MlčouÅ¡ková; Ondrej Beláň; Máté Gyimesi; Gábor M Harami ...
Pathogenic CTC1 mutations cause global genome instabilities under replication stress border= 
Yuan Wang ; Weihang Chai
Rif1 acts through Protein Phosphatase 1 but independent of replication timing to suppress telomere extension in budding yeast border= 
Sylwia Kedziora; Vamsi K Gali; Rosemary HC Wilson; Kate RM Clark; Conrad A Nieduszynski ...
DNA lesions proximity modulates damage tolerance pathways in Escherichia coli border= 
Élodie Chrabaszcz ; Luisa Laureti; Vincent Pagès
Cytotoxic and mutagenic properties of alkyl phosphotriester lesions in Escherichia coli cells border= 
Jiabin Wu; Pengcheng Wang; Yinsheng Wang
GAA¢TTC repeat expansion in human cells is mediated by mismatch repair complex MutLgamma and depends upon the endonuclease domain in MLH3 isoform one border= 
Anasheh Halabi ; Kayla T B Fuselier; Ed Grabczyk
Quantifying the stability of oxidatively damaged DNA by single-molecule DNA stretching border= 
Micah J McCauley; Leah Furman; Catherine A Dietrich; Ioulia Rouzina ; Megan E Núñez ...
Molecular Biology
Protein plasticity driven by disorder and collapse governs the heterogeneous binding of CytR to DNA border= 
Sneha Munshi; Soundhararajan Gopi; Sandhyaa Subramanian; Luis A Campos; Athi N Naganathan
A novel transcript isoform of STING that sequesters cGAMP and dominantly inhibits innate nucleic acid sensing border= 
Pei-Hui Wang ; Sin-Yee Fung; Wei-Wei Gao; Jian-Jun Deng; Yun Cheng ...
A multi-landing pad DNA integration platform for mammalian cell engineering border= 
Leonid Gaidukov; Liliana Wroblewska ; Brian Teague; Tom Nelson; Xin Zhang ...
Primed CRISPR adaptation in Escherichia coli cells does not depend on conformational changes in the Cascade effector complex detected in Vitro border=  
Andrey Krivoy; Marius Rutkauskas; Konstantin Kuznedelov ; Olga Musharova; Christophe Rouillon ...
Hrp48 and eIF3d contribute to msl-2 mRNA translational repression border= 
Emilia Szostak; Marina García-Beyaert; Tanit Guitart; Antoine Graindorge ; Olga Coll ...
Nucleic Acid Enzymes
A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance border= 
Thomas Germe; Judit Vörös; Frederic Jeannot; Thomas Taillier; Robert A Stavenger ...
Unveiling the pathway to Z-DNA in the protein-induced B'Z transition border= 
Sook Ho Kim ; So-Hee Lim; Ae-Ree Lee; Do Hoon Kwon; Hyun Kyu Song ...
The Zn-finger domain of human PrimPol is required to stabilize the initiating nucleotide during DNA priming border= 
María I Martínez-Jiménez ; Patricia A Calvo; Sara García-Gómez; Susana Guerra-González; Luis Blanco
Targeting IS608 transposon integration to highly specific sequences by structure-based transposon engineering border= 
Natalia Rosalía Morero; Cecilia Zuliani; Banushree Kumar; Aleksandra Bebel; Sachi Okamoto ...
Crystal structure and mutational analysis of Mycobacterium smegmatis FenA highlight active site amino acids and three metal ions essential for flap endonuclease and 5² exonuclease activities border= 
Maria Loressa Uson ; Ayala Carl; Yehuda Goldgur; Stewart Shuman
RNA and RNA-protein complexes
Translation initiation of alphavirus mRNA reveals new insights into the topology of the 48S initiation complex border= 
René Toribio; Irene Díaz-López; Jasminka Boskovic; Iván Ventoso
Unstructured 5²-tails act through ribosome standby to override inhibitory structure at ribosome binding sites border= 
Maaike Sterk; Cédric Romilly; E Gerhart H Wagner
An unexpected RNA distal interaction mode found in an essential region of the hepatitis C virus genome border= 
Ángel Cantero-Camacho ; José Gallego
LncRNA-OIS1 regulates DPP4 activation to modulate senescence induced by RAS border= 
Li Li; Pieter C van Breugel; Fabricio Loayza-Puch; Alejandro Pineiro Ugalde; Gozde Korkmaz ...
Human La binds mRNAs through contacts to the poly(A) tail border= 
Jyotsna Vinayak ; Stefano A Marrella; Rawaa H Hussain; Leonid Rozenfeld; Karine Solomon ...
Integrator subunit 4 is a ˜Symplekin-like' scaffold that associates with INTS9/11 to form the Integrator cleavage module border= 
Todd R Albrecht ; Sergey P Shevtsov; Yixuan Wu; Lauren G Mascibroda; Natoya J Peart ...
A translational silencing function of MCPIP1/Regnase-1 specified by the target site context border= 
Gesine Behrens; Reinhard Winzen ; Nina Rehage; Anneke Dörrie; Monika Barsch ...
Loss of RNA-binding protein HuR facilitates cellular senescence through posttranscriptional regulation of TIN2 mRNA border= 
Ji Hoon Lee; Misun Jung; Juyeong Hong ; Mi Kyung Kim; In Kwon Chung
Structural Biology
A structurally conserved motif in gamma -herpesvirus uracil-DNA glycosylases elicits duplex nucleotide-flipping border= 
Christopher Earl; Claire Bagnéris; Kara Zeman; Ambrose Cole ; Tracey Barrett ...
Pursuing origins of (poly)ethylene glycol-induced G-quadruplex structural modulations border= 
Marko Trajkovski; Tamaki Endoh; Hisae Tateishi-Karimata; Tatsuya Ohyama; Shigenori Tanaka ...
Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1 border= 
Giedrius Sasnauskas ; Kotryna KauneckaitÄ-; Virginijus Siksnys
A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance border= 
Thomas Germe; Judit Vörös; Frederic Jeannot; Thomas Taillier; Robert A Stavenger ...
Methods Online
In vitro isolation of small-molecule-binding aptamers with intrinsic dye-displacement functionality border= 
Haixiang Yu; Weijuan Yang; Obtin Alkhamis; Juan Canoura; Kyung-Ae Yang ...
Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets border= 
Jarkko Toivonen ; Teemu Kivioja; Arttu Jolma; Yimeng Yin; Jussi Taipale ...
SEASTAR: systematic evaluation of alternative transcription start sites in RNA border= 
Zhiyi Qin; Peter Stoilov ; Xuegong Zhang; Yi Xing
RNentropy: an entropy-based tool for the detection of significant variation of gene expression across multiple RNA-Seq experiments border= 
Federico Zambelli; Francesca Mastropasqua; Ernesto Picardi; Anna Maria D'Erchia ; Graziano Pesole ...
IW-Scoring: an Integrative Weighted Scoring framework for annotating and prioritizing genetic variations in the noncoding genome border= 
Jun Wang; Abu Z Dayem Ullah; Claude Chelala
A small, portable RNA device for the control of exon skipping in mammalian cells border= 
Marc Vogel; Julia E Weigand; Britta Kluge; Manuel Grez; Beatrix Suess
OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes border= 
Enrique Vidal; François le Dily; Javier Quilez; Ralph Stadhouders; Yasmina Cuartero ...
Reconstructing spatial organizations of chromosomes through manifold learning border= 
Guangxiang Zhu ; Wenxuan Deng; Hailin Hu; Rui Ma; Sai Zhang ...
Darwin Assembly: fast, efficient, multi-site bespoke mutagenesis border= 
Christopher Cozens; Vitor B Pinheiro
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