Subject: Nucleic Acids Research Table of Contents for 25 January 2018 ------=_Part_2121549636.1516989708045 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/mc47e-ddwmj1-66q6ox34/) [[BannerToken]] [[AlertTitleToken]] [[SelfServeTextToken]] [[FirstAdvertisingToken]] [[TOCMainToken]] Unsubscribe (http://click.skem1.com/form?mc47e--ply5-66q6ox30&sl=tq&t=5)Manage email alerts (http://click.skem1.com/click/mc47e-ddwmj2-66q6ox35/) 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/mc47e-ddwmj3-66q6ox36/) [[BottomAdvertisingToken]] This email is intended for bionet@evol.mcmaster.ca. ------=_Part_2121549636.1516989708045 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Nucleic Acids Research  
Volume 46 Issue 2
 
25 January 2018
 
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NAR Breakthrough Article
 
 
 
Reconstitution of the CstF complex unveils a regulatory role for CstF-50 in recognition of 3²-end processing signals border= 
 
Wen Yang; Peter L Hsu; Fan Yang; Jae-Eun Song ; Gabriele Varani
 
 
SURVEY AND SUMMARY
 
 
 
Mechanisms of bacterial DNA replication restart border= 
 
Tricia A Windgassen; Sarah R Wessel; Basudeb Bhattacharyya; James L Keck
 
 
Tyrosyl'DNA phosphodiesterases: rescuing the genome from the risks of relaxation border= 
 
Ajinkya S Kawale; Lawrence F Povirk
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Rolling circle amplification shows a sinusoidal template length-dependent amplification bias border= 
 
Bastian Joffroy ; Yavuz O Uca; Domen PreĊĦern; Jonathan P. K Doye; Thorsten L Schmidt
 
 
Veratramine modulates AP-1-dependent gene transcription by directly binding to programmable DNA border= 
 
Fang Bai; Kangdong Liu ; Huiliang Li; Jiawei Wang; Junsheng Zhu ...
 
 
 
 
Computational Biology
 
 
 
Energetic funnel facilitates facilitated diffusion border= 
 
Massimo Cencini; Simone Pigolotti
 
 
Dynamics of the excised base release in thymine DNA glycosylase during DNA repair process border= 
 
Lin-Tai Da; Yi Shi; Guodong Ning ; Jin Yu
 
 
Data Resources and Analyses
 
 
 
Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues border= 
 
Alejandro Reyes; Wolfgang Huber
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Dynamic reorganization of open chromatin underlies diverse transcriptomes during spermatogenesis border= 
 
So Maezawa; Masashi Yukawa; Kris G Alavattam; Artem Barski ; Satoshi H Namekawa
 
 
The histone variant H2A.Z promotes initiation of meiotic recombination in fission yeast border= 
 
Shintaro Yamada; Kazuto Kugou; Da-Qiao Ding; Yurika Fujita; Yasushi Hiraoka ...
 
 
 
 
Paf1 and Ctr9, core components of the PAF1 complex, maintain low levels of telomeric repeat containing RNA border= 
 
Joana Rodrigues; David Lydall
 
 
Single-molecule compaction of megabase-long chromatin molecules by multivalent cations border= 
 
Anatoly Zinchenko ; Nikolay V Berezhnoy; Sai Wang; William M Rosencrans; Nikolay Korolev ...
 
 
DNA knots occur in intracellular chromatin border= 
 
Antonio Valdés; Joana Segura ; Sílvia Dyson; Belén Martínez-García; Joaquim Roca
 
 
The regulatory G4 motif of the Kirsten ras (KRAS) gene is sensitive to guanine oxidation: implications on transcription border=  
 
Susanna Cogoi; Annalisa Ferino; Giulia Miglietta ; Erik B Pedersen; Luigi E Xodo
 
 
Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes border= 
 
Diego Duchi; Kristofer Gryte; Nicole C Robb; Zakia Morichaud ; Carol Sheppard ...
 
 
Genome Integrity, Repair and Replication
 
 
 
Acetylation of 53BP1 dictates the DNA double strand break repair pathway border= 
 
Xiang Guo; Yongtai Bai; Meimei Zhao; Mei Zhou; Qinjian Shen ...
 
 
Fission yeast Ccq1 is a modulator of telomerase activity border= 
 
Christine A Armstrong ; Vera Moiseeva; Laura C Collopy; Siân R Pearson; Tomalika R Ullah ...
 
 
LncRNA lnc-RI regulates homologous recombination repair of DNA double-strand breaks by stabilizing RAD51 mRNA as a competitive endogenous RNA border= 
 
Liping Shen; Qi Wang ; Ruixue Liu; Zhongmin Chen; Xueqing Zhang ...
 
 
Nuclear poly(A)-binding protein 1 is an ATM target and essential for DNA double-strand break repair border= 
 
Michal Gavish-Izakson; Bhagya Bhavana Velpula; Ran Elkon; Rosario Prados-Carvajal; Georgina D Barnabas ...
 
 
Differential RPA-1 and RAD-51 recruitment in vivo throughout the C. elegans germline, as revealed by laser microirradiation border= 
 
Emily Koury; Kailey Harrell; Sarit Smolikove
 
 
Genomics
 
 
 
Trypanosomatid mitochondrial RNA editing: dramatically complex transcript repertoires revealed with a dedicated mapping tool border= 
 
Evgeny S Gerasimov ; Anna A Gasparyan; Iosif Kaurov; Boris Tichý; Maria D Logacheva ...
 
 
Molecular Biology
 
 
 
Influence of thermodynamically unfavorable secondary structures on DNA hybridization kinetics border= 
 
Hiroaki Hata; Tetsuro Kitajima ; Akira Suyama
 
 
Improving CRISPR'Cas specificity with chemical modifications in single-guide RNAs border= 
 
Daniel E Ryan; David Taussig; Israel Steinfeld; Smruti M Phadnis; Benjamin D Lunstad ...
 
 
The C-terminal domain of p53 orchestrates the interplay between non-covalent and covalent poly(ADP-ribosyl)ation of p53 by PARP1 border= 
 
Arthur Fischbach; Annika Krüger; Stephanie Hampp; Greta Assmann; Lisa Rank ...
 
 
USP9X controls translation efficiency via deubiquitination of eukaryotic translation initiation factor 4A1 border= 
 
Zengxia Li; Zhao Cheng ; Chaerkady Raghothama; Zhaomeng Cui; Kaiyu Liu ...
 
 
Nucleic Acid Enzymes
 
 
 
The non-specific adenine DNA methyltransferase M.EcoGII border=  
 
Iain A Murray; Richard D Morgan; Yvette Luyten ; Alexey Fomenkov; Ivan R. Corrêa, Jr ...
 
 
Editing activity for eliminating mischarged tRNAs is essential in mammalian mitochondria border= 
 
Taru Hilander; Xiao-Long Zhou; Svetlana Konovalova; Fu-Ping Zhang ; Liliya Euro ...
 
 
TopA, the Sulfolobus solfataricus topoisomerase III, is a decatenase border= 
 
Anna H Bizard; Xi Yang; Hélène Débat; Jonathan M Fogg; Lynn Zechiedrich ...
 
 
Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR'Cas effector complexes border= 
 
Marnix Vlot ; Joep Houkes; Silke J A Lochs; Daan C Swarts; Peiyuan Zheng ...
 
 
RNA and RNA-protein complexes
 
 
 
Specific G-quadruplex ligands modulate the alternative splicing of Bcl-X border= 
 
Carika Weldon; Justine G Dacanay ; Vijay Gokhale; Peda Venkat L Boddupally; Isabelle Behm-Ansmant ...
 
 
Structural rearrangements in mRNA upon its binding to human 80S ribosomes revealed by EPR spectroscopy border=  
 
Alexey A Malygin; Dmitri M Graifer; Maria I Meschaninova ; Alya G Venyaminova; Ivan O Timofeev ...
 
 
Efficient RNA pseudouridylation by eukaryotic H/ACA ribonucleoproteins requires high affinity binding and correct positioning of guide RNA border= 
 
Evan A Caton; Erin K Kelly; Rajashekhar Kamalampeta; Ute Kothe
 
 
Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs border= 
 
Diogo M Ribeiro; Andreas Zanzoni ; Andrea Cipriano; Riccardo Delli Ponti; Lionel Spinelli ...
 
 
Structural Biology
 
 
 
Biochemical and structural characterization of a novel cooperative binding mode by Pit-1 with CATT repeats in the macrophage migration inhibitory factor promoter border= 
 
Sorabh Agarwal ; Thomas Yoonsang Cho
 
 
E-motif formed by extrahelical cytosine bases in DNA homoduplexes of trinucleotide and hexanucleotide repeats border= 
 
Feng Pan; Yuan Zhang; Viet Hoang Man; Christopher Roland; Celeste Sagui
 
 
Capped RNA primer binding to influenza polymerase and implications for the mechanism of cap-binding inhibitors border= 
 
Alexander Pflug ; Stephanie Gaudon; Patricia Resa-Infante; Mathilde Lethier; Stefan Reich ...
 
 
Structural and functional analysis of an OB-fold in human Ctc1 implicated in telomere maintenance and bone marrow syndromes border= 
 
Prashanth K Shastrula ; Cory T Rice; Zhuo Wang; Paul M Lieberman; Emmanuel Skordalakes
 
 
Synthetic Biology and Bioengineering
 
 
 
Complete motif analysis of sequence requirements for translation initiation at non-AUG start codons border= 
 
Alexander J Diaz de Arce; William L Noderer; Clifford L Wang
 
 
Binary control of enzymatic cleavage of DNA origami by structural antideterminants border= 
 
Alex Stopar; Lucia Coral; Stefano Di Giacomo; Abimbola F Adedeji; Matteo Castronovo
 
 
Methods Online
 
 
 
Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells border= 
 
Yi Cui; Dehong Hu; Lye Meng Markillie; William B Chrisler; Matthew J Gaffrey ...
 
 
Fluorescently-tagged human eIF3 for single-molecule spectroscopy border= 
 
Alex G Johnson ; Alexey N Petrov; Gabriele Fuchs; Karim Majzoub; Rosslyn Grosely ...
 
 
Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions border= 
 
André L Martins; Ninad M Walavalkar; Warren D Anderson; Chongzhi Zang; Michael J Guertin
 
 
Partial bisulfite conversion for unique template sequencing border= 
 
Vijay Kumar; Julie Rosenbaum; Zihua Wang; Talitha Forcier ; Michael Ronemus ...
 
 
FreePSI: an alignment-free approach to estimating exon-inclusion ratios without a reference transcriptome border= 
 
Jianyu Zhou; Shining Ma; Dongfang Wang; Jianyang Zeng; Tao Jiang
 
 
A bacterial three-hybrid assay detects Escherichia coli Hfq'sRNA interactions in vivo border= 
 
Katherine E Berry ; Ann Hochschild
 
 
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