Subject: Nucleic Acids Research Table of Contents for 16 November 2017 ------=_Part_1430106649.1511025089216 Content-Type: text/plain;charset=UTF-8 Oxford Academic [[HeaderAdvertisingToken]] https://silverchair.emailcampaigns.net/media/50/509735/OUP/oxford_logo.jpg?g72331686458 (http://click.skem1.com/click/kz8eo-col97n-66q6ox32/) [[BannerToken]] [[AlertTitleToken]] [[SelfServeTextToken]] [[FirstAdvertisingToken]] [[TOCMainToken]] Unsubscribe (http://click.skem1.com/form?kz8eo--ply5-66q6ox31&sl=tq&t=5)Manage email alerts (http://click.skem1.com/click/kz8eo-col97o-66q6ox33/) Written requests to unsubscribe can be sent to: Journals Marketing, Oxford University Press, Great Clarendon Street, Oxford, OX2 6DP, UK. The content of this email is protected by copyright. https://silverchair.emailcampaigns.net/media/50/509735/OUP/oxforde_university.jpg?g72331733632 (http://click.skem1.com/click/kz8eo-col97p-66q6ox34/) [[BottomAdvertisingToken]] This email is intended for bionet@evol.mcmaster.ca. ------=_Part_1430106649.1511025089216 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Nucleic Acids Research  
Volume 45 Issue 20
 
16 November 2017
 
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NAR Breakthrough Article
 
 
 
A single active site in the mariner transposase cleaves DNA strands of opposite polarity border= 
 
Corentin Claeys Bouuaert; Ronald Chalmers
 
 
SURVEY AND SUMMARY
 
 
 
Systematic classification of the His-Me finger superfamily border=  
 
Jagoda Jablonska; Dorota Matelska; Kamil Steczkiewicz ; Krzysztof Ginalski
 
 
Confronting the catalytic dark matter encoded by sequenced genomes border= 
 
Kenneth W. Ellens; Nils Christian; Charandeep Singh; Venkata P. Satagopam; Patrick May ...
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Measuring deaminated nucleotide surveillance enzyme ITPA activity with an ATP-releasing nucleotide chimera border= 
 
Debin Ji ; Elena I. Stepchenkova; Jian Cui; Miriam R. Menezes; Youri I. Pavlov ...
 
 
Exponential propagation of large circular DNA by reconstitution of a chromosome-replication cycle border= 
 
Masayuki Su'etsugu; Hiraku Takada ; Tsutomu Katayama; Hiroko Tsujimoto
 
 
 
 
2▓-Fluoroarabinonucleic acid modification traps G-quadruplex and i-motif structures in human telomeric DNA border= 
 
Hala Abou Assi; Roberto El-Khoury; Carlos González; Masad J. Damha
 
 
Computational Biology
 
 
 
Computational construction of 3D chromatin ensembles and prediction of functional interactions of alpha-globin locus from 5C data border= 
 
Gamze Gürsoy ; Yun Xu; Amy L. Kenter; Jie Liang
 
 
cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches border= 
 
Daniel E. Martin-Herranz; António J. M. Ribeiro; Felix Krueger ; Janet M. Thornton; Wolf Reik ...
 
 
TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs border= 
 
Zhen Tan; Yinghan Fu; Gaurav Sharma; David H. Mathews
 
 
Transcriptional accuracy modeling suggests two-step proofreading by RNA polymerase border= 
 
Harriet Mellenius; Måns Ehrenberg
 
 
 
 
Data Resources and Analyses
 
 
 
N6-adenine DNA methylation is associated with the linker DNA of H2A.Z-containing well-positioned nucleosomes in Pol II-transcribed genes in Tetrahymena border= 
 
Yuanyuan Wang; Xiao Chen; Yalan Sheng; Yifan Liu; Shan Gao
 
 
Cis-regulatory landscapes of four cell types of the retina border= 
 
Dominik Hartl ; Arnaud R. Krebs; Josephine Jüttner; Botond Roska; Dirk Schübeler
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Histone H1 depletion triggers an interferon response in cancer cells via activation of heterochromatic repeats border= 
 
Andrea Izquierdo-Bouldstridge; Alberto Bustillos; Carles Bonet-Costa; Patricia Aribau-Miralbés; Daniel García-Gomis ...
 
 
Multi-dimensional histone methylations for coordinated regulation of gene expression under hypoxia border=  
 
Seongyeol Lee; Jieon Lee; Sehyun Chae ; Yunwon Moon; Ho-Youl Lee ...
 
 
A pathway for low zinc homeostasis that is conserved in animals and acts in parallel to the pathway for high zinc homeostasis border= 
 
Nicholas Dietrich; Daniel L. Schneider; Kerry Kornfeld
 
 
Histone chaperone HIRA deposits histone H3.3 onto foreign viral DNA and contributes to anti-viral intrinsic immunity border= 
 
Taranjit Singh Rai; Mandy Glass; John J. Cole; Mohammad I. Rather; Morgan Marsden ...
 
 
Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies border= 
 
Dinesh Manandhar; Lingyun Song; Ami Kabadi; Jennifer B. Kwon; Lee E. Edsall ...
 
 
PP32 and SET/TAF-Ibeta proteins regulate the acetylation of newly synthesized histone H4 border= 
 
Francisco Saavedra; Carlos Rivera; Elizabeth Rivas; Paola Merino; Daniel Garrido ...
 
 
The stability of an mRNA is influenced by its concentration: a potential physical mechanism to regulate gene expression border= 
 
Sébastien Nouaille; Sophie Mondeil; Anne-Laure Finoux; Claire Moulis; Laurence Girbal ...
 
 
The nuclear mitotic apparatus protein NuMA controls rDNA transcription and mediates the nucleolar stress response in a p53-independent manner border= 
 
Swaathi Jayaraman ; Shirisha Chittiboyina; Yunfeng Bai; Patricia C. Abad; Pierre-Alexandre Vidi ...
 
 
Genome Integrity, Repair and Replication
 
 
 
Cooperative RecA clustering: the key to efficient homology searching border= 
 
Andrew J. Lee; Rajan Sharma ; Jamie K. Hobbs; Christoph Wälti
 
 
Molecular mechanisms by which oxidative DNA damage promotes telomerase activity border= 
 
Hui-Ting Lee; Arindam Bose; Chun-Ying Lee; Patricia L. Opresko ; Sua Myong
 
 
Dna2 initiates resection at clean DNA double-strand breaks border= 
 
Sharad C. Paudyal; Shan Li; Hong Yan; Tony Hunter; Zhongsheng You
 
 
A cell-penetrating antibody inhibits human RAD51 via direct binding border= 
 
Audrey Turchick ; Denise C. Hegan; Ryan B. Jensen; Peter M. Glazer
 
 
Genomics
 
 
 
Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803 border= 
 
Joaquín Giner-Lamia; Rocío Robles-Rengel ; Miguel A. Hernández-Prieto; M. Isabel Muro-Pastor; Francisco J. Florencio ...
 
 
Quantitating translational control: mRNA abundance-dependent and independent contributions and the mRNA sequences that specify them 
 
Jingyi Jessica Li; Guo-Liang Chew; Mark D. Biggin
 
 
Molecular Biology
 
 
 
FANCI and FANCD2 have common as well as independent functions during the cellular replication stress response border= 
 
Elizabeth L. Thompson; Jung E. Yeo; Eun-A Lee; Yinan Kan; Maya Raghunandan ...
 
 
Signal recognition particle binds to translating ribosomes before emergence of a signal anchor sequence border= 
 
Evan Mercier; Wolf Holtkamp; Marina V. Rodnina; Wolfgang Wintermeyer
 
 
Human Argonaute3 has slicer activity border= 
 
Mi Seul Park ; Hong-Duc Phan; Florian Busch; Samantha H. Hinckley; James A. Brackbill ...
 
 
RecQ helicase triggers a binding mode change in the SSB'DNA complex to efficiently initiate DNA unwinding  
 
Maria Mills; Gábor M. Harami; Yeonee Seol ; Máté Gyimesi; Máté Martina ...
 
 
Nucleic Acid Enzymes
 
 
 
The siRNA suppressor RTL1 is redox-regulated through glutathionylation of a conserved cysteine in the double-stranded-RNA-binding domain border=  
 
Cyril Charbonnel; Adnan K. Niazi; Emilie Elvira-Matelot ; El┼╝bieta Nowak; Matthias Zytnicki ...
 
 
C-terminal lysine repeats in Streptomyces topoisomerase I stabilize the enzyme'DNA complex and confer high enzyme processivity border= 
 
Agnieszka Strzałka; Marcin J. Szafran; Terence Strick; Dagmara Jakimowicz
 
 
Enzyme cycling contributes to efficient induction of genome mutagenesis by the cytidine deaminase APOBEC3B border= 
 
Madison B. Adolph; Robin P. Love; Yuqing Feng; Linda Chelico
 
 
RNA and RNA-protein complexes
 
 
 
Competition between translation initiation factor eIF5 and its mimic protein 5MP determines non-AUG initiation rate genome-wide border= 
 
Leiming Tang; Jacob Morris; Ji Wan; Chelsea Moore ; Yoshihiko Fujita ...
 
 
Cdk5rap1-mediated 2-methylthio-N6-isopentenyladenosine modification is absent from nuclear-derived RNA species border= 
 
Md. Fakruddin; Fan Yan Wei; Shohei Emura; Shigeru Matsuda; Takehiro Yasukawa ...
 
 
Novel mechanisms of eIF2B action and regulation by eIF2alpha phosphorylation border= 
 
Andrew M. Bogorad ; Kai Ying Lin; Assen Marintchev
 
 
The SMAD3 transcription factor binds complex RNA structures with high affinity border= 
 
Thayne H. Dickey; Anna M. Pyle
 
 
Structural Biology
 
 
 
The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module border=  
 
David Dilworth; Santosh K. Upadhyay; Pierre Bonnafous ; Amiirah Bibi Edoo; Sarah Bourbigot ...
 
 
Structural basis for the specific recognition of 18S rRNA by APUM23 border= 
 
Hongyu Bao; Na Wang; Chongyuan Wang; Yiyang Jiang ; Jiuyang Liu ...
 
 
Structural insights into RNA unwinding and degradation by RNase R border= 
 
Lee-Ya Chu; Tung-Ju Hsieh; Bagher Golzarroshan; Yi-Ping Chen; Sashank Agrawal ...
 
 
Mechanistic insight into the assembly of the HerA'NurA helicase'nuclease DNA end resection complex border= 
 
Zainab Ahdash ; Andy M. Lau; Robert Thomas Byrne; Katja Lammens; Alexandra Stüetzer ...
 
 
Synthetic Biology and Bioengineering
 
 
 
CRISPR/Cas9-mediated gene knockout is insensitive to target copy number but is dependent on guide RNA potency and Cas9/sgRNA threshold expression level 
 
Garmen Yuen; Fehad J. Khan ; Shaojian Gao; Jayne M. Stommel; Eric Batchelor ...
 
 
Corrigendum
 
 
 
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 ...
 
 
2▓-Fluoroarabinonucleic acid modification traps G-quadruplex and i-motif structures in human telomeric DNA border= 
 
Hala Abou Assi; Roberto El-Khoury; Carlos González; Masad J. Damha
 
 
Methods Online
 
 
 
Bidirectional approaches for optogenetic regulation of gene expression in mammalian cells using Arabidopsis cryptochrome 2 border=  
 
Gopal P. Pathak; Jessica I. Spiltoir; Camilla Höglund ; Lauren R. Polstein; Sari Heine-Koskinen ...
 
 
REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes border= 
 
Elvis Ndah; Veronique Jonckheere; Adam Giess; Eivind Valen ; Gerben Menschaert ...
 
 
Towards enhanced and interpretable clustering/classification in integrative genomics border= 
 
Yang Young Lu; Jinchi Lv; Jed A. Fuhrman; Fengzhu Sun
 
 
Individual-specific edge-network analysis for disease prediction border= 
 
Xiangtian Yu; Jingsong Zhang ; Shaoyan Sun; Xin Zhou; Tao Zeng ...
 
 
CRISPR/Cas9-based genome editing for simultaneous interference with gene expression and protein stability border= 
 
Virginia Martínez; Ida Lauritsen; Tonja Hobel; Songyuan Li; Alex Toftgaard Nielsen ...
 
 
Optimized light-inducible transcription in mammalian cells using Flavin Kelch-repeat F-box1/GIGANTEA and CRY2/CIB1 border= 
 
Jose R. Quejada; Seon-Hye E. Park; Daniel W. Awari; Fan Shi; Hannah E. Yamamoto ...
 
 
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