Subject: Nucleic Acids Research Table of Contents for 7 July 2017 Oxford Academic
 
 
 
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New issue alert
 
Nucleic Acids Research  
Volume 45 Issue 12
 
7 July 2017
 
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SURVEY AND SUMMARY
 
 
 
Comprehensive classification of the PIN domain-like superfamily border= 
 
Dorota Matelska; Kamil Steczkiewicz; Krzysztof Ginalski
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Newly characterized interaction stabilizes DNA structure: oligoethylene glycols stabilize G-quadruplexes CH'Ďeuro interactions border= 
 
Hisae Tateishi-Karimata ; Tatsuya Ohyama; Takahiro Muraoka; Peter Podbevsek; Adam M. Wawro ...
 
 
Modulation of cyclobutane thymine photodimer formation in T11 -tracts in rotationally phased nucleosome core particles and DNA minicircles border= 
 
Kesai Wang; John-Stephen A. Taylor
 
 
Chemical ligation of oligonucleotides using an electrophilic phosphorothioester border= 
 
Hideto Maruyama ; Ryota Oikawa; Mayu Hayakawa; Shono Takamori; Yasuaki Kimura ...
 
 
Computational Biology
 
 
 
The PhytoClust tool for metabolic gene clusters discovery in plant genomes border= 
 
Nadine Töpfer; Lisa-Maria Fuchs ; Asaph Aharoni
 
 
 
 
Identifying transposon insertions and their effects from RNA-sequencing data border= 
 
Julian R. de Ruiter ; Sjors M. Kas; Eva Schut; David J. Adams; Marco J. Koudijs ...
 
 
Universal attenuators and their interactions with feedback loops in gene regulatory networks border= 
 
Dianbo Liu; Luca Albergante ; Timothy J. Newman
 
 
Data Resources and Analyses
 
 
 
ChiPPI: a novel method for mapping chimeric protein'protein interactions uncovers selection principles of protein fusion events in cancer border= 
 
Milana Frenkel-Morgenstern; Alessandro Gorohovski; Somnath Tagore; Vaishnovi Sekar; Miguel Vazquez ...
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
A network of cis and trans interactions is required for ParB spreading border= 
 
Dan Song ; Kristen Rodrigues; Thomas G.W. Graham; Joseph J. Loparo
 
 
Methyl-CpG binding domain protein 1 regulates localization and activity of Tet1 in a CXXC3 domain-dependent manner border= 
 
Peng Zhang; Cathia Rausch; Florian D. Hastert ; Boyana Boneva; Alina Filatova ...
 
 
 
 
Identification of HDA15-PIF1 as a key repression module directing the transcriptional network of seed germination in the dark border= 
 
Dachuan Gu; Chia-Yang Chen; Minglei Zhao; Linmao Zhao; Xuewu Duan ...
 
 
Fbxl19 recruitment to CpG islands is required for Rnf20-mediated H2B mono-ubiquitination border= 
 
Bum-Kyu Lee ; Jiwoon Lee; Wenwen Shen; Catherine Rhee; Haewon Chung ...
 
 
The 2-mu m plasmid encoded protein Raf1 regulates both stability and copy number of the plasmid by blocking the formation of the Rep1'Rep2 repressor complex border= 
 
Syed M. A. Rizvi ; Hemant K. Prajapati; Purba Nag; Santanu K. Ghosh
 
 
The ATP-dependent chromatin remodeler Chd1 is recruited by transcription elongation factors and maintains H3K4me3/H3K36me3 domains at actively transcribed and spliced genes border=  
 
Yaelim Lee; Daechan Park; Vishwanath R. Iyer
 
 
In mammalian foetal testes, SOX9 regulates expression of its target genes by binding to genomic regions with conserved signatures border= 
 
Massilva Rahmoun ; Rowena Lavery; Sabine Laurent-Chaballier; Nicolas Bellora; Gayle K. Philip ...
 
 
A non-canonical site reveals the cooperative mechanisms of microRNA-mediated silencing border= 
 
Mathieu N. Flamand; Hin Hark Gan ; Vinay K. Mayya; Kristin C. Gunsalus; Thomas F. Duchaine
 
 
Genome Integrity, Repair and Replication
 
 
 
Quaternary interactions and supercoiling modulate the cooperative DNA binding of AGT border= 
 
Manana Melikishvili; Michael G. Fried
 
 
DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein border= 
 
José A. Morin ; Fernando Cerrón; Javier Jarillo; Elena Beltran-Heredia; Grzegorz L. Ciesielski ...
 
 
Functional characterization and architecture of recombinant yeast SWR1 histone exchange complex border= 
 
Chia-Liang Lin; Yuriy Chaban ; David M. Rees; Elizabeth A. McCormack; Lorraine Ocloo ...
 
 
An intact Mcm10 coiled-coil interaction surface is important for origin melting, helicase assembly and the recruitment of Pol-alpha to Mcm2'7 border=  
 
Patricia Perez-Arnaiz; Irina Bruck; Max K. Colbert ; Daniel L. Kaplan
 
 
Replication studies of carboxymethylated DNA lesions in human cells border= 
 
Jun Wu; Pengcheng Wang; Lin Li; Nicole L. Williams; Debin Ji ...
 
 
Genomics
 
 
 
Genome-wide mRNA processing in methanogenic archaea reveals post-transcriptional regulation of ribosomal protein synthesis border= 
 
Lei Qi ; Lei Yue; Deqin Feng; Fengxia Qi; Jie Li ...
 
 
Molecular Biology
 
 
 
Compaction and condensation of DNA mediated by the C-terminal domain of Hfq border= 
 
Antoine Malabirade; Kai Jiang ; Krzysztof Kubiak; Alvaro Diaz-Mendoza; Fan Liu ...
 
 
Ribosomal selection of mRNAs with degenerate initiation triplets border= 
 
He Chengguang; Paola Sabatini; Letizia Brandi; Anna M. Giuliodori ; Cynthia L. Pon ...
 
 
eIF5A facilitates translation termination globally and promotes the elongation of many non polyproline-specific tripeptide sequences border= 
 
Vicent Pelechano; Paula Alepuz
 
 
Nucleic Acid Enzymes
 
 
 
Coiled-coil interactions mediate serine integrase directionality border= 
 
Kushol Gupta; Robert Sharp; Jimmy B. Yuan; Huiguang Li ; Gregory D. Van Duyne
 
 
DNA substrate recognition and processing by the full-length human UPF1 helicase border= 
 
Saba Dehghani-Tafti; Cyril M. Sanders
 
 
Self-protective responses to norvaline-induced stress in a leucyl-tRNA synthetase editing-deficient yeast strain border= 
 
Quan-Quan Ji; Zhi-Peng Fang; Qing Ye; Cheng-Wu Chi ; En-Duo Wang
 
 
RNA
 
 
 
Two ribosome recruitment sites direct multiple translation events within HIV1 Gag open reading frame border= 
 
Jules Deforges; Sylvain de Breyne; Melissa Ameur; Nathalie Ulryck; Nathalie Chamond ...
 
 
ALKBH1 is an RNA dioxygenase responsible for cytoplasmic and mitochondrial tRNA modifications border= 
 
Layla Kawarada ; Takeo Suzuki; Takayuki Ohira; Shoji Hirata; Kenjyo Miyauchi ...
 
 
Environment-dependent regulation of spliceosome activity by the LSM2-8 complex in Arabidopsis border= 
 
Cristian Carrasco-López; Tamara Hernández-Verdeja; Carlos Perea-Resa; David Abia; Rafael Catalá ...
 
 
A novel double kink-turn module in euryarchaeal RNase P RNAs border= 
 
Lien B. Lai; Akiko Tanimoto; Stella M. Lai; Wen-Yi Chen ; Ila A. Marathe ...
 
 
Protein-only RNase P function in Escherichia coli: viability, processing defects and differences between PRORP isoenzymes border= 
 
Markus Gößringer; Marcus Lechner; Nadia Brillante; Christoph Weber; Walter Rossmanith ...
 
 
Implication of the box C/D snoRNP assembly factor Rsa1p in U3 snoRNP assembly border= 
 
Benjamin Rothé ; Xavier Manival; Nicolas Rolland; Christophe Charron; Véronique Senty-Ségault ...
 
 
Translational control and Rho-dependent transcription termination are intimately linked in riboswitch regulation border= 
 
Laurène Bastet; Adrien Chauvier; Navjot Singh; Antony Lussier; Anne-Marie Lamontagne ...
 
 
Structural Biology
 
 
 
G-quadruplex structure of an anti-proliferative DNA sequence border=  
 
Ngoc Quang Do; Wan Jun Chung; Thi Hong Anh Truong ; Brahim Heddi; Anh Tuân Phan
 
 
Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation border= 
 
Xiao Xiao; Hanjing Yang; Vagan Arutiunian; Yao Fang ; Guillaume Besse ...
 
 
Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state border= 
 
Ilya A. Osterman; Nelli F. Khabibullina; Ekaterina S. Komarova; Pavel Kasatsky; Victor G. Kartsev ...
 
 
Synthetic Biology and Bioengineering
 
 
 
Dynamics of sequestration-based gene regulatory cascades border= 
 
Tatenda Shopera ; William R. Henson; Tae Seok Moon
 
 
Enhancing multiplex genome editing by natural transformation (MuGENT) via inactivation of ssDNA exonucleases border= 
 
Triana N. Dalia; Soo Hun Yoon; Elisa Galli; Francois-Xavier Barre ; Christopher M. Waters ...
 
 
Corrigendum
 
 
 
Two ribosome recruitment sites direct multiple translation events within HIV1 Gag open reading frame border= 
 
Jules Deforges; Sylvain de Breyne; Melissa Ameur; Nathalie Ulryck; Nathalie Chamond ...
 
 
Not5-dependent co-translational assembly of Ada2 and Spt20 is essential for functional integrity of SAGA border= 
 
Sari Kassem ; Zoltan Villanyi; Martine A. Collart
 
 
Erratum
 
 
 
Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation border= 
 
Xiao Xiao; Hanjing Yang; Vagan Arutiunian; Yao Fang ; Guillaume Besse ...
 
 
Methods Online
 
 
 
LncFunNet: an integrated computational framework for identification of functional long noncoding RNAs in mouse skeletal muscle cells border= 
 
Jiajian Zhou; Suyang Zhang; Huating Wang; Hao Sun
 
 
Distributed biotin'streptavidin transcription roadblocks for mapping cotranscriptional RNA folding border= 
 
Eric J. Strobel; Kyle E. Watters ; Yuri Nedialkov; Irina Artsimovitch; Julius B. Lucks
 
 
SPA-LN: a scoring function of ligand'nucleic acid interactions via optimizing both specificity and affinity border= 
 
Zhiqiang Yan; Jin Wang
 
 
TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads border=  
 
Petr Novák; Laura Ă vila Robledillo; Andrea KoblĂ­Ĺľková ; Iva Vrbová; Pavel Neumann ...
 
 
Poly(A)-ClickSeq: click-chemistry for next-generation 3Î"-end sequencing without RNA enrichment or fragmentation border= 
 
Andrew Routh; Ping Ji; Elizabeth Jaworski; Zheng Xia ; Wei Li ...
 
 
Characterizing exogenous mRNA delivery, trafficking, cytoplasmic release and RNA'protein correlations at the level of single cells border= 
 
Jonathan L. Kirschman; Sushma Bhosle; Daryll Vanover; Emmeline L. Blanchard; Kristin H. Loomis ...
 
 
Gene set selection via LASSO penalized regression (SLPR) border= 
 
H. Robert Frost ; Christopher I. Amos
 
 
Using high-throughput barcode sequencing to efficiently map connectomes border= 
 
Ian D. Peikon; Justus M. Kebschull; Vasily V. Vagin; Diana I. Ravens; Yu-Chi Sun ...
 
 
High-purity circular RNA isolation method (RPAD) reveals vast collection of intronic circRNAs 
 
Amaresh C. Panda; Supriyo De ; Ioannis Grammatikakis; Rachel Munk; Xiaoling Yang ...
 
 
Synthetic mRNA devices that detect endogenous proteins and distinguish mammalian cells border= 
 
Shunsuke Kawasaki; Yoshihiko Fujita; Takashi Nagaike; Kozo Tomita ; Hirohide Saito
 
 
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