Subject: Nucleic Acids Research Table of Contents for 13 October 2017 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Nucleic Acids Research  
Volume 45 Issue 18
 
13 October 2017
 
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NAR Breakthrough Article
 
 
 
Subtelomeres constitute a safeguard for gene expression and chromosome homeostasis border= 
 
Sanki Tashiro; Yuki Nishihara; Kazuto Kugou; Kunihiro Ohta ; Junko Kanoh
 
 
SURVEY AND SUMMARY
 
 
 
Nuclear speckles: molecular organization, biological function and role in disease border= 
 
Lukasz Galganski; Martyna O. Urbanek; Wlodzimierz J. Krzyzosiak
 
 
Dicer-independent processing of small RNA duplexes: mechanistic insights and applications border= 
 
Elena Herrera-Carrillo; Ben Berkhout
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
DNA mimics of red fluorescent proteins (RFP) based on G-quadruplex-confined synthetic RFP chromophores border= 
 
Guangfu Feng; Chao Luo ; Haibo Yi; Lin Yuan; Bin Lin ...
 
 
Computational Biology
 
 
 
MAPPIN: a method for annotating, predicting pathogenicity and mode of inheritance for nonsynonymous variants border=  
 
Nehal Gosalia; Aris N. Economides; Frederick E. Dewey ; Suganthi Balasubramanian
 
 
 
 
Computational characterization of chromatin domain boundary-associated genomic elements border= 
 
Seungpyo Hong ; Dongsup Kim
 
 
Functional 5≤ UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks border= 
 
Mathieu Lavallée-Adam; Philippe Cloutier; Benoit Coulombe; Mathieu Blanchette
 
 
Gene-regulatory interactions in embryonic stem cells represent cell-type specific gene regulatory programs border= 
 
Misook Ha; Soondo Hong
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
An RNA editing/dsRNA binding-independent gene regulatory mechanism of ADARs and its clinical implication in cancer border= 
 
Lihua Qi ; Yangyang Song; Tim Hon Man Chan; Henry Yang; Chi Ho Lin ...
 
 
Fractionation iCLIP detects persistent SR protein binding to conserved, retained introns in chromatin, nucleoplasm and cytoplasm border= 
 
Mattia Brugiolo ; Valentina Botti; Na Liu; Michaela M√ľller-McNicoll; Karla M. Neugebauer
 
 
 
 
Identification of Plagl1/Zac1 binding sites and target genes establishes its role in the regulation of extracellular matrix genes and the imprinted gene network border= 
 
Annie Varrault ; Christelle Dantec; Anne Le Digarcher; La√ętitia Chotard; Benoit Bilanges ...
 
 
A sequence-specific core promoter-binding transcription factor recruits TRF2 to coordinately transcribe ribosomal protein genes border= 
 
Douglas G. Baumann ; David S. Gilmour
 
 
PARP1 controls KLF4-mediated telomerase expression in stem cells and cancer cells border= 
 
Meng-Hsun Hsieh; Yi-Ting Chen; You-Tzung Chen; Yi-Hsuan Lee; Jean Lu ...
 
 
Single-molecule kinetic analysis of HP1-chromatin binding reveals a dynamic network of histone modification and DNA interactions border= 
 
Louise C. Bryan ; Daniel R. Weilandt; Andreas L. Bachmann; Sinan Kilic; Carolin C. Lechner ...
 
 
The yeast 2-mu m plasmid Raf protein contributes to plasmid inheritance by stabilizing the Rep1 and Rep2 partitioning proteins border= 
 
Mary E. McQuaid; Jordan B. Pinder; Niroshaathevi Arumuggam; Jessica S. C. Lacoste; Joyce S. K. Chew ...
 
 
CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality border= 
 
Helen Hoffmeister; Andreas Fuchs; Fabian Erdel ; Sophia Pinz; Regina Gröbner-Ferreira ...
 
 
Genome Integrity, Repair and Replication
 
 
 
Dynamic stepwise opening of integron attC DNA hairpins by SSB prevents toxicity and ensures functionality border= 
 
Maj Svea Grieb; Aleksandra Nivina; Bevan L. Cheeseman; Andreas Hartmann ; Didier Mazel ...
 
 
Replication stress-induced endogenous DNA damage drives cellular senescence induced by a sub-lethal oxidative stress border= 
 
Gireedhar Venkatachalam; Uttam Surana; Marie-Véronique Clément
 
 
Protein phosphatase 1 and phosphatase 1 nuclear targeting subunit-dependent regulation of DNA-dependent protein kinase and non-homologous end joining border=  
 
Songli Zhu; Laura A. Fisher; Tadayoshi Bessho ; Aimin Peng
 
 
Homeostatic nuclear RAGE'ATM interaction is essential for efficient DNA repair border= 
 
Varun Kumar; Thomas Fleming; Stefan Terjung; Christian Gorzelanny; Christoffer Gebhardt ...
 
 
H2AX facilitates classical non-homologous end joining at the expense of limited nucleotide loss at repair junctions border= 
 
Yi-Li Feng ; Ji-Feng Xiang; Si-Cheng Liu; Tao Guo; Guo-Fang Yan ...
 
 
Genomics
 
 
 
Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts border= 
 
Robin van der Lee; Laurens Wiel; Teunis J.P. van Dam; Martijn A. Huynen
 
 
Molecular Biology
 
 
 
Nucleic acid binding proteins affect the subcellular distribution of phosphorothioate antisense oligonucleotides border=  
 
Jeffrey K. Bailey; Wen Shen; Xue-hai Liang ; Stanley T. Crooke
 
 
Dynamic nucleoplasmic and nucleolar localization of mammalian RNase H1 in response to RNAP I transcriptional R-loops border= 
 
Wen Shen; Hong Sun; Cheryl L. De Hoyos; Jeffrey K. Bailey; Xue-hai Liang ...
 
 
The Cdc45/RecJ-like protein forms a complex with GINS and MCM, and is important for DNA replication in Thermococcus kodakarensis border= 
 
Mariko Nagata; Sonoko Ishino; Takeshi Yamagami; Hiromi Ogino; Jan-Robert Simons ...
 
 
Nuclear poly(A) binding protein 1 (PABPN1) and Matrin3 interact in muscle cells and regulate RNA processing border= 
 
Ayan Banerjee; Katherine E. Vest ; Grace K. Pavlath; Anita H. Corbett
 
 
RNA guanine-7 methyltransferase catalyzes the methylation of cytoplasmically recapped RNAs border= 
 
Jackson B. Trotman; Andrew J. Giltmier; Chandrama Mukherjee; Daniel R. Schoenberg
 
 
Nucleic Acid Enzymes
 
 
 
Allosteric regulation of Csx1, a type IIIB-associated CARF domain ribonuclease by RNAs carrying a tetraadenylate tail border= 
 
Wenyuan Han ; Saifu Pan; Blanca López-Méndez; Guillermo Montoya; Qunxin She
 
 
Plant organellar DNA polymerases are replicative and translesion DNA synthesis polymerases border= 
 
Noe Baruch-Torres; Luis G. Brieba
 
 
Plant organellar DNA primase-helicase synthesizes RNA primers for organellar DNA polymerases using a unique recognition sequence border= 
 
Antolín Peralta-Castro; Noe Baruch-Torres; Luis G. Brieba
 
 
Force-activated DNA substrates for probing individual proteins interacting with single-stranded DNA 
 
Stephen R. Okoniewski; Lyle Uyetake; Thomas T. Perkins
 
 
RNA and RNA-protein complexes
 
 
 
Small RNA profiling in Chlamydomonas: insights into chloroplast RNA metabolism border=  
 
Marina Cavaiuolo; Richard Kuras; FrancisźAndr√© Wollman ; Yves Choquet; Olivier Vallon
 
 
CRISPR'Cas9-mediated functional dissection of 3≤-UTRs border= 
 
Wenxue Zhao; David Siegel; Anne Biton; Olivier Le Tonqueze; Noah Zaitlen ...
 
 
Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions border= 
 
Zasha Weinberg ; Christina E. L√ľnse; Keith A. Corbino; Tyler D. Ames; James W. Nelson ...
 
 
The Rio1p ATPase hinders premature entry into translation of late pre-40S pre-ribosomal particles border= 
 
Kamila Belhabich-Baumas; Clément Joret ; Beáta E. Jády; Célia Plisson-Chastang; Ramtin Shayan ...
 
 
Biochemical and single-molecule analyses of the RNA silencing suppressing activity of CrPV-1A border= 
 
Mariko Watanabe; Hiro-oki Iwakawa; Hisashi Tadakuma; Yukihide Tomari
 
 
Structural Biology
 
 
 
Structural insights into RapZ-mediated regulation of bacterial amino-sugar metabolism border= 
 
Grecia M. Gonzalez; Svetlana Durica-Mitic; Steven W. Hardwick; Martin C. Moncrieffe; Marcus Resch ...
 
 
Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry border= 
 
Ying-Ren Wang ; Shin-Fu Chen; Chyuan-Chuan Wu; Yi-Wen Liao; Te-Sheng Lin ...
 
 
The intricate network between the p34 and p44 subunits is central to the activity of the transcription/DNA repair factor TFIIH border= 
 
Laura Radu; Elisabeth Schoenwetter; Cathy Braun; Julien Marcoux; Wolfgang Koelmel ...
 
 
Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis border=  
 
Kailu Yang; Jeng-Yih Chang; Zhicheng Cui ; Xiaojun Li; Ran Meng ...
 
 
Synthetic Biology and Bioengineering
 
 
 
De novo design and synthesis of a 30-cistron translation-factor module border= 
 
Tyson R. Shepherd; Liping Du; Josefine Liljeruhm; Samudyata ; Jinfan Wang ...
 
 
In silico design of context-responsive mammalian promoters with user-defined functionality border= 
 
Adam J. Brown; Suzanne J. Gibson; Diane Hatton; David C. James
 
 
Corrigendum
 
 
 
Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry border= 
 
Ying-Ren Wang; Shin-Fu Chen; Chyuan-Chuan Wu; Yi-Wen Liao; Te-Sheng Lin ...
 
 
HH-MOTiF: de novo detection of short linear motifs in proteins by Hidden Markov Model comparisons border= 
 
Roman Prytuliak; Michael Volkmer; Markus Meier; Bianca H. Habermann
 
 
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. M√ľller; Irene A. Chen
 
 
Methods Online
 
 
 
Novel cell surface luciferase reporter for high-throughput yeast one-hybrid screens border= 
 
Katia Bonaldi; Zheng Li ; S. Earl Kang; Ghislain Breton; Jose L. Pruneda-Paz
 
 
Tandem phage-display for the identification of non-overlapping binding pairs of recombinant affinity reagents border= 
 
Kevin T. Gorman; Lauren C. Roby; Allison Giuffre; Renhua Huang; Brian K. Kay
 
 
Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations border= 
 
Eric Marinier; Rahat Zaheer; Chrystal Berry; Kelly A. Weedmark; Michael Domaratzki ...
 
 
Entirely enzymatic nanofabrication of DNA'protein conjugates border= 
 
Giulio Bernardinelli ; Björn Högberg
 
 
Fidelity of RNA templated end-joining by chlorella virus DNA ligase and a novel iLock assay with improved direct RNA detection accuracy border= 
 
Tomasz Krzywkowski; Mats Nilsson
 
 
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