Subject: Nucleic Acids Research Table of Contents for 30 November 2018 ------=_Part_744307471.1543856624315 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_744307471.1543856624315 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Nucleic Acids Research  
Volume 46 Issue 21
 
30 November 2018
 
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NAR Breakthrough Article
 
 
 
Crosstalk among Set1 complex subunits involved in H2B ubiquitylation-dependent H3K4 methylation border= 
 
Jongcheol Jeon; Robert K McGinty; Tom W Muir; Jung-Ae Kim; Jaehoon Kim
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Principles of chemical geometry underlying chiral selectivity in RNA minihelix aminoacylation border= 
 
Tadashi Ando; Shunichi Takahashi ; Koji Tamura
 
 
 
Computational Biology
 
 
 
CLIPick: a sensitive peak caller for expression-based deconvolution of HITS-CLIP signals border= 
 
Sihyung Park; Seung Hyun Ahn ; Eun Sol Cho; You Kyung Cho; Eun-Sook Jang ...
 
 
 
Data Resources and Analyses
 
 
 
Proteomic profiling and functional characterization of post-translational modifications of the fission yeast RNA exosome border= 
 
Caroline Telekawa ; François-Michel Boisvert; François Bachand
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers border= 
 
Shaliu Fu ; Qin Wang; Jill E Moore; Michael J Purcaro; Henry E Pratt ...
 
 
DYRK1A interacts with histone acetyl transferase p300 and CBP and localizes to enhancers border=  
 
Shanshan Li; Chu Xu; Yinkun Fu ; Pin-Ji Lei; Yanhua Yao ...
 
 
Interplay between transcription regulators RUNX1 and FUBP1 activates an enhancer of the oncogene c-KIT and amplifies cell proliferation border= 
 
Lydie Debaize; Hélène Jakobczyk ; Stéphane Avner; Jérémie Gaudichon; Anne-Gaëlle Rio ...
 
 
An auxin controls bacterial antibiotics production border= 
 
Miguel A Matilla; Abdelali Daddaoua; Andrea Chini ; Bertrand Morel; Tino Krell
 
 
HiCDB: a sensitive and robust method for detecting contact domain boundaries border=  
 
Fengling Chen; Guipeng Li; Michael Q Zhang ; Yang Chen
 
 
Dot1 promotes H2B ubiquitination by a methyltransferase-independent mechanism border=  
 
Tibor van Welsem; Tessy Korthout; Reggy Ekkebus ; Dominique Morais; Thom M Molenaar ...
 
 
Distinctive structural basis for DNA recognition by the fission yeast Zn2Cys6 transcription factor Pho7 and its role in phosphate homeostasis border= 
 
Angad Garg; Yehuda Goldgur ; Beate Schwer; Stewart Shuman
 
 
 
Genome Integrity, Repair and Replication
 
 
 
Single-molecule DREEM imaging reveals DNA wrapping around human mitochondrial single-stranded DNA binding protein 
 
Parminder Kaur; Matthew J Longley; Hai Pan; Hong Wang; William C Copeland
 
 
The bacterial Mre11'Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions border= 
 
Jan-Hinnerk Saathoff ; Lisa Käshammer; Katja Lammens; Robert Thomas Byrne; Karl-Peter Hopfner
 
 
Structural basis of 5 flap recognition and protein'protein interactions of human flap endonuclease 1 border=  
 
Hong Xu; Rongyi Shi; Wanchun Han ; Jiahui Cheng; Xiaoli Xu ...
 
 
Bre1-dependent H2B ubiquitination promotes homologous recombination by stimulating histone eviction at DNA breaks border=  
 
Sihao Zheng; Dan Li; Zhen Lu ; Guangxue Liu; Meng Wang ...
 
 
Regulation of HLTF-mediated PCNA polyubiquitination by RFC and PCNA monoubiquitination levels determines choice of damage tolerance pathway border= 
 
Yuji Masuda ; Satoshi Mitsuyuki; Rie Kanao; Asami Hishiki; Hiroshi Hashimoto ...
 
 
 
Genomics
 
 
 
Single-cell stabilization method identifies gonadotrope transcriptional dynamics and pituitary cell type heterogeneity border= 
 
Frederique Ruf-Zamojski ; Yongchao Ge; Venugopalan Nair; Michel Zamojski; Hanna Pincas ...
 
 
 
Molecular Biology
 
 
 
Homodimerization regulates an endothelial specific signature of the SOX18 transcription factor border= 
 
Mehdi Moustaqil; Frank Fontaine; Jeroen Overman; Alex McCann; Timothy L Bailey ...
 
 
Modulation of MKNK2 alternative splicing by splice-switching oligonucleotides as a novel approach for glioblastoma treatment border= 
 
Maxim Mogilevsky; Odelia Shimshon; Saran Kumar; Adi Mogilevsky; Eli Keshet ...
 
 
Genome-wide identification of genic and intergenic neuronal DNA regions bound by Tau protein under physiological and stress conditions border= 
 
Houda Benhelli-Mokrani ; Zeyni Mansuroglu; Alban Chauderlier; Benoit Albaud; David Gentien ...
 
 
Human GTPBP10 is required for mitoribosome maturation border= 
 
Priyanka Maiti; Hyun-Jung Kim; Ya-Ting Tu ; Antoni Barrientos
 
 
 
Nucleic Acid Enzymes
 
 
 
Excision-reintegration at a pneumococcal phase-variable restriction-modification locus drives within- and between-strain epigenetic differentiation and inhibits gene acquisition border= 
 
Min Jung Kwun ; Marco R Oggioni; Megan De Ste Croix; Stephen D Bentley; Nicholas J Croucher
 
 
Substrate specificity of human apurinic/apyrimidinic endonuclease APE1 in the nucleotide incision repair pathway border=  
 
Alexandra A Kuznetsova; Anna G Matveeva; Alexander D Milov ; Yuri N Vorobjev; Sergei A Dzuba ...
 
 
Streptococcus suis contains multiple phase-variable methyltransferases that show a discrete lineage distribution border= 
 
John M Atack; Lucy A Weinert ; Alexander W Tucker; Asma U Husna; Thomas M Wileman ...
 
 
Region 3.2 of the σ factor controls the stability of rRNA promoter complexes and potentiates their repression by DksA border= 
 
Danil Pupov ; Ivan Petushkov; Daria Esyunina; Katsuhiko S Murakami; Andrey Kulbachinskiy
 
 
 
RNA and RNA-protein complexes
 
 
 
Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1 border= 
 
Yuichiro Nomura; Daniel Roston ; Eric J Montemayor; Qiang Cui; Samuel E Butcher
 
 
The RNA exosome contributes to gene expression regulation during stem cell differentiation border=  
 
Marta Lloret-Llinares; Evdoxia Karadoulama; Yun Chen ; Luke A Wojenski; Geno J Villafano ...
 
 
Enterovirus 71 antagonizes the inhibition of the host intrinsic antiviral factor A3G border=  
 
Zhaolong Li; Shanshan Ning; Xing Su ; Xin Liu; Hong Wang ...
 
 
The APT complex is involved in non-coding RNA transcription and is distinct from CPF border=  
 
Michael Lidschreiber; Ashley D Easter; Sofia Battaglia ; Juan B Rodríguez-Molina; Ana Casañal ...
 
 
A Rev'CBP80'eIF4AI complex drives Gag synthesis from the HIV-1 unspliced mRNA border=  
 
Daniela Toro-Ascuy; Bárbara Rojas-Araya; Francisco García-de-Gracia ; Cecilia Rojas-Fuentes; Camila Pereira-Montecinos ...
 
 
Monitored eCLIP: high accuracy mapping of RNA-protein interactions border=  
 
Rémi Hocq; Janio Paternina; Quentin Alasseur ; Auguste Genovesio; Hervé Le Hir
 
 
Sustenance of Escherichia coli on a single tRNAMet border=  
 
Ashwin Govindan; Shreya Ahana Ayyub; Umesh Varshney
 
 
Comprehensive analysis of the BC200 ribonucleoprotein reveals a reciprocal regulatory function with CSDE1/UNR border=  
 
Evan P Booy; Ewan KS McRae; Peyman Ezzati ; Taegi Choi; Daniel Gussakovsky ...
 
 
Analysis of NRAS RNA G-quadruplex binding proteins reveals DDX3X as a novel interactor of cellular G-quadruplex containing transcripts border= 
 
Barbara Herdy ; Clemens Mayer; Dhaval Varshney; Giovanni Marsico; Pierre Murat ...
 
 
 
Structural Biology
 
 
 
NMR structure of a G-quadruplex formed by four d(G4C2 ) repeats: insights into structural polymorphism border= 
 
Jasna Brčić; Janez Plavec
 
 
Stacking-induced fluorescence increase reveals allosteric interactions through DNA border=  
 
Michael J Morten; Sergio G Lopez; I Emilie Steinmark ; Aidan Rafferty; Steven W Magennis
 
 
High-resolution DNA quadruplex structure containing all the A-, G-, C-, T-tetrads border=  
 
Hehua Liu; Rui Wang; Xiang Yu ; Fusheng Shen; Wenxian Lan ...
 
 
Structural, functional and biological insights into the role of Mycobacterium tuberculosis VapBC11 toxin'antitoxin system: targeting a tRNase to tackle mycobacterial adaptation border= 
 
Amar Deep; Prabhakar Tiwari ; Sakshi Agarwal; Soni Kaundal; Saqib Kidwai ...
 
 
 
Methods Online
 
 
 
CellBIC: bimodality-based top-down clustering of single-cell RNA sequencing data reveals hierarchical structure of the cell type border= 
 
Junil Kim ; Diana E Stanescu; Kyoung Jae Won
 
 
Hercules: a profile HMM-based hybrid error correction algorithm for long reads border=  
 
Can Firtina; Ziv Bar-Joseph; Can Alkan ; A Ercument Cicek
 
 
Assessing genome assembly quality using the LTR Assembly Index (LAI) border=  
 
Shujun Ou; Jinfeng Chen; Ning Jiang
 
 
Modular 5-UTR hexamers for context-independent tuning of protein expression in eukaryotes border=  
 
Søren D Petersen; Jie Zhang; Jae S Lee ; Tadas Jakočiūnas; Lise M Grav ...
 
 
SLING: a tool to search for linked genes in bacterial datasets border= 
 
Gal Horesh; Alexander Harms; Cinzia Fino ; Leopold Parts; Kenn Gerdes ...
 
 
Capping-RACE: a simple, accurate, and sensitive 5 RACE method for use in prokaryotes border=  
 
Fang Liu; Ke Zheng; Huan-Chun Chen ; Zheng-Fei Liu
 
 
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