Subject: Nucleic Acids Research Table of Contents for 21 August 2017 Oxford Academic
 
 
 
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New issue alert
 
Nucleic Acids Research  
Volume 45 Issue 14
 
21 August 2017
 
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SURVEY AND SUMMARY
 
 
 
The role of poly ADP-ribosylation in the first wave of DNA damage response border= 
 
Chao Liu; Aditi Vyas; Muzaffer A. Kassab; Anup K. Singh ; Xiaochun Yu
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs border= 
 
Daniel Mutisya; Travis Hardcastle; Samwel K. Cheruiyot; Pradeep S. Pallan; Scott D. Kennedy ...
 
 
Monomolecular G-quadruplex structures with inversion of polarity sites: new topologies and potentiality border= 
 
Antonella Virgilio ; Annapina Russo; Teresa Amato; Giulia Russo; Luciano Mayol ...
 
 
Computational Biology
 
 
 
Analysis of in vitro evolution reveals the underlying distribution of catalytic activity among random sequences border= 
 
Abe Pressman; Janina E. Moretti ; Gregory W. Campbell; Ulrich F. Müller; Irene A. Chen
 
 
Synchronized switching of multiple toxin'antitoxin modules by (p)ppGpp fluctuation border= 
 
Chengzhe Tian; Szabolcs Semsey; Namiko Mitarai
 
 
 
 
Cell-to-cell variability and robustness in S-phase duration from genome replication kinetics border= 
 
Qing Zhang; Federico Bassetti ; Marco Gherardi; Marco Cosentino Lagomarsino
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Quantitative specificity of STAT1 and several variants border= 
 
Basab Roy; Zheng Zuo; Gary D. Stormo
 
 
Evolutionary re-wiring of p63 and the epigenomic regulatory landscape in keratinocytes and its potential implications on species-specific gene expression and phenotypes border= 
 
Isha Sethi ; Christian Gluck; Huiqing Zhou; Michael J. Buck; Satrajit Sinha
 
 
H2B ubiquitylation and the histone chaperone Asf1 cooperatively mediate the formation and maintenance of heterochromatin silencing border= 
 
Meng-Ying Wu ; Chia-Yeh Lin; Hsin-Yi Tseng; Fei-Man Hsu; Pao-Yang Chen ...
 
 
Methylation of human eukaryotic elongation factor alpha (eEF1A) by a member of a novel protein lysine methyltransferase family modulates mRNA translation border= 
 
Magnus E. Jakobsson ; Jędrzej Małecki; Benedikt S. Nilges; Anders Moen; Sebastian A. Leidel ...
 
 
 
 
LDB1-mediated enhancer looping can be established independent of mediator and cohesin 
 
Ivan Krivega; Ann Dean
 
 
A novel isoform of TET1 that lacks a CXXC domain is overexpressed in cancer border= 
 
Charly R. Good; Jozef Madzo; Bela Patel; Shinji Maegawa ; Nora Engel ...
 
 
Bacterial RNA polymerase caps RNA with various cofactors and cell wall precursors border= 
 
Christina Julius; Yulia Yuzenkova
 
 
Genome Integrity, Repair and Replication
 
 
 
Monitoring of the spatial and temporal dynamics of BER/SSBR pathway proteins, including MYH, UNG2, MPG, NTH1 and NEIL1-3, during DNA replication border= 
 
Karine Ø. Bj⊘rås; Mirta M. L. Sousa; Animesh Sharma; Davi M. Fonseca; Caroline K. S⊘gaard ...
 
 
Bacillus subtilis DNA polymerases, PolC and DnaE, are required for both leading and lagging strand synthesis in SPP1 origin-dependent DNA replication border= 
 
Elena M. Seco; Silvia Ayora
 
 
Telomere shortening triggers a feedback loop to enhance end protection border= 
 
Chia-Wei Yang; Shun-Fu Tseng; Chia-Jung Yu; Chia-Yu Chung; Cheng-Yen Chang ...
 
 
Characterization of a coupled DNA replication and translesion synthesis polymerase supraholoenzyme from archaea border= 
 
Matthew T. Cranford ; Aurea M. Chu; Joshua K. Baguley; Robert J. Bauer; Michael A. Trakselis
 
 
The identification of FANCD2 DNA binding domains reveals nuclear localization sequences border= 
 
Joshi Niraj; Marie-Christine Caron ; Karine Drapeau; Stéphanie Bérubé; Laure Guitton-Sert ...
 
 
Genomics
 
 
 
Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin border= 
 
Zaida Vergara; Joana Sequeira-Mendes; Jordi Morata; Ramón Peiró; Elizabeth Hénaff ...
 
 
Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation border= 
 
Virag Sharma; Michael Hiller
 
 
Molecular Biology
 
 
 
Functional and structural analysis of AT-specific minor groove binders that disrupt DNA'protein interactions and cause disintegration of the Trypanosoma brucei kinetoplast border= 
 
Cinthia R. Millan; Francisco J. Acosta-Reyes ; Laura Lagartera; Godwin U. Ebiloma; Leandro Lemgruber ...
 
 
Amino acid substrates impose polyamine, eIF5A, or hypusine requirement for peptide synthesis 
 
Byung-Sik Shin; Takayuki Katoh; Erik Gutierrez; Joo-Ran Kim ; Hiroaki Suga ...
 
 
BRD4 inhibitors block telomere elongation border= 
 
Steven Wang; Alexandra M. Pike; Stella S. Lee; Margaret A. Strong; Carla J. Connelly ...
 
 
Comparative analysis of chimeric ZFP-, TALE- and Cas9-piggyBac transposases for integration into a single locus in human cells 
 
Wentian Luo ; Daniel L. Galvan; Lauren E. Woodard; Dan Dorset; Shawn Levy ...
 
 
Nucleic Acid Enzymes
 
 
 
Restriction endonuclease triggered bacterial apoptosis as a mechanism for long time survival border= 
 
Easa Nagamalleswari; Sandhya Rao ; Kommireddy Vasu; Valakunja Nagaraja
 
 
CgII cleaves DNA using a mechanism distinct from other ATP-dependent restriction endonucleases border= 
 
Paulius Toliusis; Mindaugas Zaremba; Arunas Silanskas; Mark D. Szczelkun ; Virginijus Siksnys
 
 
ATP hydrolysis provides functions that promote rejection of pairings between different copies of long repeated sequences border= 
 
Claudia Danilowicz; Laura Hermans; Vincent Coljee; Chantal Prévost; Mara Prentiss
 
 
RNA
 
 
 
The double-stranded RNA binding protein RDE-4 can act cell autonomously during feeding RNAi in C. elegans border= 
 
Pravrutha Raman ; Soriayah M. Zaghab; Edward C. Traver; Antony M. Jose
 
 
An in vivo genetic screen for genes involved in spliced leader trans-splicing indicates a crucial role for continuous de novo spliced leader RNP assembly border=  
 
Lucas Philippe; George C. Pandarakalam; Rotimi Fasimoye ; Neale Harrison; Bernadette Connolly ...
 
 
Codon usage regulates protein structure and function by affecting translation elongation speed in Drosophila cells border= 
 
Fangzhou Zhao; Chien-hung Yu; Yi Liu
 
 
Visualization of conformational variability in the domains of long single-stranded RNA molecules border= 
 
Jamie L. Gilmore; Aiko Yoshida ; James A. Hejna; Kunio Takeyasu
 
 
Alternative splicing of CNOT7 diversifies CCR4'NOT functions border= 
 
Clément Chapat; Kamel Chettab; Pierre Simonet; Peng Wang ; Pierre De La Grange ...
 
 
Autoregulation of RBM10 and cross-regulation of RBM10/RBM5 via alternative splicing-coupled nonsense-mediated decay border= 
 
Yue Sun; Yufang Bao; Wenjian Han; Fan Song; Xianfeng Shen ...
 
 
Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best border= 
 
Max Ward ; Amitava Datta; Michael Wise; David H. Mathews
 
 
Structural Biology
 
 
 
DRB4 dsRBD1 drives dsRNA recognition in Arabidopsis thaliana tasi/siRNA pathway border=  
 
Sai Chaitanya Chiliveri; Ramdas Aute; Upasana Rai ; Mandar V. Deshmukh
 
 
Functional details of the Mycobacterium tuberculosis VapBC26 toxin-antitoxin system based on a structural study: insights into unique binding and antibiotic peptides border= 
 
Sung-Min Kang; Do-Hee Kim; Ki-Young Lee; Sung Jean Park ; Hye-Jin Yoon ...
 
 
Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation border= 
 
Tofayel Ahmed; Jian Shi; Shashi Bhushan
 
 
Tethering not required: the glucocorticoid receptor binds directly to activator protein-1 recognition motifs to repress inflammatory genes border= 
 
Emily R. Weikum ; Ian Mitchelle S. de Vera; Jerome C. Nwachukwu; William H. Hudson; Kendall W. Nettles ...
 
 
A data-driven structural model of hSSB1 (NABP2/OBFC2B) self-oligomerization border= 
 
Christine Touma; Mark N. Adams ; Nicholas W. Ashton; Michael Mizzi; Serene El-Kamand ...
 
 
Synthetic Biology and Bioengineering
 
 
 
Crystallographic analyses illustrate significant plasticity and efficient recoding of meganuclease target specificity border= 
 
Rachel Werther; Jazmine P. Hallinan; Abigail R. Lambert; Kyle Havens; Mark Pogson ...
 
 
Control of serine integrase recombination directionality by fusion with the directionality factor border= 
 
Femi J. Olorunniji; Arlene L. McPherson; Susan J. Rosser; Margaret C.M. Smith; Sean D. Colloms ...
 
 
Corrigendum
 
 
 
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
 
 
Methods Online
 
 
 
Multiplexed analysis of fixed tissue RNA using Ligation in situ Hybridization border= 
 
Joel J. Credle; Christopher Y. Itoh ; Tiezheng Yuan; Rajni Sharma; Erick R. Scott ...
 
 
A deep boosting based approach for capturing the sequence binding preferences of RNA-binding proteins from high-throughput CLIP-seq data border=  
 
Shuya Li; Fanghong Dong; Yuexin Wu ; Sai Zhang; Chen Zhang ...
 
 
FASTmiR: an RNA-based sensor for in vitro quantification and live-cell localization of small RNAs border= 
 
Kun Huang; Francis Doyle; Zachary E. Wurz; Scott A. Tenenbaum ; Reza K. Hammond ...
 
 
Prioritizing tests of epistasis through hierarchical representation of genomic redundancies border= 
 
Tyler Cowman; Mehmet Koyutürk
 
 
COSINE: non-seeding method for mapping long noisy sequences border= 
 
Pegah Tootoonchi Afshar; Wing Hung Wong
 
 
Determination of tRNA aminoacylation levels by high-throughput sequencing border= 
 
Molly E. Evans; Wesley C. Clark; Guanqun Zheng; Tao Pan
 
 
Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics border= 
 
Mary C. Clay; Laura R. Ganser ; Dawn K. Merriman; Hashim M. Al-Hashimi
 
 
Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo border= 
 
Laura E. Ritchey; Zhao Su; Yin Tang; David C. Tack ; Sarah M. Assmann ...
 
 
CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures border= 
 
Shahidul Islam; Ping Ge; Shaojie Zhang
 
 
Digital direct detection of microRNAs using single molecule arrays border= 
 
Limor Cohen; Mark R. Hartman; Aaron Amardey-Wellington; David R. Walt
 
 
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