Subject: Nucleic Acids Research Table of Contents for 25 January 2019 ------=_Part_1360727059.1548609366106 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1360727059.1548609366106 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Nucleic Acids Research  
Volume 47 Issue 2
 
25 January 2019
 
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Survey and Summary
 
 
 
Are TADs supercoiled? border= 
 
Dusan Racko; Fabrizio Benedetti; Julien Dorier ; Andrzej Stasiak
 
 
Temporospatial guidance of activity-dependent gene expression by microRNA: mechanisms and functional implications for neural plasticity border= 
 
Dylan Kiltschewskij ; Murray J Cairns
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Extensive CRISPR RNA modification reveals chemical compatibility and structure-activity relationships for Cas9 biochemical activity border= 
 
Daniel O'Reilly ; Zachary J Kartje; Eman A Ageely; Elise Malek-Adamian; Maryam Habibian ...
 
 
 
Data Resources and Analyses
 
 
 
Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks border= 
 
P Schäpe; MJ Kwon ; B Baumann; B Gutschmann; S Jung ...
 
 
Deciphering human ribonucleoprotein regulatory networks border= 
 
Neelanjan Mukherjee; Hans-Hermann Wessels; Svetlana Lebedeva ; Marcin Sajek; Mahsa Ghanbari ...
 
 
Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions border= 
 
Shilpa Nadimpalli Kobren ; Mona Singh
 
 
RefSeq curation and annotation of stop codon recoding in vertebrates 
 
Bhanu Rajput; Kim D Pruitt; Terence D Murphy
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
H3.3K4M destabilizes enhancer H3K4 methyltransferases MLL3/MLL4 and impairs adipose tissue development 
 
Younghoon Jang; Aaron Broun; Chaochen Wang; Young-Kwon Park; Lenan Zhuang ...
 
 
DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor border=  
 
Klára Šmídová; Alice Ziková; Jiří Pospíšil ; Marek Schwarz; Jan Bobek ...
 
 
Genome-wide function of MCM-BP in Trypanosoma brucei DNA replication and transcription border=  
 
Hee-Sook Kim
 
 
3D organization of chicken genome demonstrates evolutionary conservation of topologically associated domains and highlights unique architecture of erythrocytes' chromatin border= 
 
Veniamin Fishman ; Nariman Battulin; Miroslav Nuriddinov; Antonina Maslova; Anna Zlotina ...
 
 
Single and double box HMGB proteins differentially destabilize nucleosomes border=  
 
Micah J McCauley; Ran Huo; Nicole Becker ; Molly Nelson Holte; Uma M Muthurajan ...
 
 
Retrograde BMP signaling activates neuronal gene expression through widespread deployment of a conserved BMP-responsive cis-regulatory activation element  border= 
 
Robin Vuilleumier; Tianshun Lian ; Stephane Flibotte; Zaynah N Khan; Alisa Fuchs ...
 
 
MIR sequences recruit zinc finger protein ZNF768 to expressed genes border=  
 
Michaela Rohrmoser; Michael Kluge; Yousra Yahia ; Anita Gruber-Eber; Muhammad Ahmad Maqbool ...
 
 
DNA sequence elements required for partitioning competence of the Saccharomyces cerevisiae 2-micron plasmid STB locus border= 
 
Mary E McQuaid; Elizabeth J Polvi ; Melanie J Dobson
 
 
The OTUD5'UBR5 complex regulates FACT-mediated transcription at damaged chromatin border=  
 
Angelo de Vivo; Anthony Sanchez; Jose Yegres ; Jeonghyeon Kim; Sylvia Emly ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
RPA resolves conflicting activities of accessory proteins during reconstitution of Dmc1-mediated meiotic recombination border= 
 
Yuen-Ling Chan ; Annie Zhang; Benjamin P Weissman; Douglas K Bishop
 
 
RNF8 mediates NONO degradation following UV-induced DNA damage to properly terminate ATR-CHK1 checkpoint signaling border=  
 
Rakesh Deshar; Wonjin Yoo; Eun-Bee Cho ; Sungjoo Kim; Jong-Bok Yoon
 
 
Excision of uracil from DNA by hSMUG1 includes strand incision and processing border=  
 
Marina Alexeeva; Marivi N Moen; Kristin Grøsvik ; Almaz N Tesfahun; Xiang Ming Xu ...
 
 
Mrc1 and Tof1 prevent fragility and instability at long CAG repeats by their fork stabilizing function border=  
 
Lionel Gellon; Simran Kaushal; Jorge Cebrián ; Mayurika Lahiri; Sergei M Mirkin ...
 
 
 
Molecular Biology
 
 
 
Role of the uS9/yS16 C-terminal tail in translation initiation and elongation in Saccharomyces cerevisiae  border= 
 
Supriya Jindal; Arnab Ghosh ; Amra Ismail; Nishant Singh; Anton A Komar
 
 
ITCH nuclear translocation and H1.2 polyubiquitination negatively regulate the DNA damage response border=  
 
Lufen Chang; Lei Shen; Hu Zhou ; Jing Gao; Hangyi Pan ...
 
 
Regulation of (p)ppGpp hydrolysis by a conserved archetypal regulatory domain border=  
 
Séverin Ronneau; Julien Caballero-Montes; Jérôme Coppine ; Aurélie Mayard; Abel Garcia-Pino ...
 
 
MEHMO syndrome mutation EIF2S3-I259M impairs initiator Met-tRNAiMet binding to eukaryotic translation initiation factor eIF2 
 
Sara K Young-Baird; Byung-Sik Shin; Thomas E Dever
 
 
 
Nucleic Acid Enzymes
 
 
 
Hexameric assembly of the AAA+ protein McrB is necessary for GTPase activity border=  
 
Neha Nirwan; Pratima Singh; Gyana Gourab Mishra ; Christopher M Johnson; Mark D Szczelkun ...
 
 
AtTrm5a catalyses 1-methylguanosine and 1-methylinosine formation on tRNAs and is important for vegetative and reproductive growth in Arabidopsis thaliana  border= 
 
Xiaohuan Jin; Zhengyi Lv ; Junbao Gao; Rui Zhang; Ting Zheng ...
 
 
 
RNA and RNA-protein complexes
 
 
 
Dynamic protein'RNA interactions in mediating splicing catalysis border=  
 
Che-Sheng Chung; Chi-Kang Tseng; Yung-Hua Lai ; Hui-Fang Wang; Andrew J Newman ...
 
 
Splicing of long non-coding RNAs primarily depends on polypyrimidine tract and 5 splice-site sequences due to weak interactions with SR proteins border= 
 
Zuzana Krchňáková ; Prasoon Kumar Thakur; Michaela Krausová; Nicole Bieberstein; Nejc Haberman ...
 
 
Stoichiometry of triple-sieve tRNA editing complex ensures fidelity of aminoacyl-tRNA formation border=  
 
Lin Chen; Akiko Tanimoto; Byung Ran So ; Marina Bakhtina; Thomas J Magliery ...
 
 
Plant RNases T2, but not Dicer-like proteins, are major players of tRNA-derived fragments biogenesis border=  
 
Cyrille Megel; Guillaume Hummel; Stéphanie Lalande ; Elodie Ubrig; Valérie Cognat ...
 
 
Quantitative fluorescence imaging determines the absolute number of locked nucleic acid oligonucleotides needed for suppression of target gene expression border= 
 
Annette Buntz ; Tobias Killian; Daniela Schmid; Heike Seul; Ulrich Brinkmann ...
 
 
Degenerate minigene library analysis enables identification of altered branch point utilization by mutant splicing factor 3B1 (SF3B1) border= 
 
Abhishek K Gupta ; Tushar Murthy; Kiran V Paul; Oscar Ramirez; Joseph B Fisher ...
 
 
 
Structural Biology
 
 
 
Exploring the effects of cosolutes and crowding on the volumetric and kinetic profile of the conformational dynamics of a poly dA loop DNA hairpin: a single-molecule FRET study border= 
 
Satyajit Patra ; Vitor Schuabb; Irena Kiesel; Jim-Marcel Knop; Rosario Oliva ...
 
 
Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family border=  
 
Giedre Tamulaitiene; Elena Manakova; Virginija Jovaisaite ; Gintautas Tamulaitis; Saulius Grazulis ...
 
 
HuR biological function involves RRM3-mediated dimerization and RNA binding by all three RRMs border=  
 
Marta Pabis; Grzegorz M Popowicz; Ralf Stehle ; David Fernández-Ramos; Sam Asami ...
 
 
Structural basis for acceptor RNA substrate selectivity of the 3 terminal uridylyl transferase Tailor border=  
 
Alena Kroupova; Anastasia Ivaşcu; Madalena M Reimão-Pinto ; Stefan L Ameres; Martin Jinek
 
 
 
Corrigendum
 
 
 
Aberrant splicing in B-cell acute lymphoblastic leukemia border=  
 
Kathryn L Black; Ammar S Naqvi; Mukta Asnani ; Katharina E Hayer; Scarlett Y Yang ...
 
 
Multi-omic and multi-view clustering algorithms: review and cancer benchmark border=  
 
Nimrod Rappoport; Ron Shamir
 
 
A protein shuttle system to target RNA into mitochondria border= 
 
François Sieber; Antonio Placido; Samira El Farouk-Ameqrane ; Anne-Marie Duchêne; Laurence Maréchal-Drouard
 
 
Molecular basis for the differential interaction of plant mitochondrial VDAC proteins with tRNAs border=  
 
Thalia Salinas; Samira El Farouk-Ameqrane; Elodie Ubrig ; Claude Sauter; Anne-Marie Duchêne ...
 
 
 
Methods Online
 
 
 
psichomics: graphical application for alternative splicing quantification and analysis border= 
 
Nuno Saraiva-Agostinho; Nuno L Barbosa-Morais
 
 
Fast and global detection of periodic sequence repeats in large genomic resources border=  
 
Hideto Mori; Daniel Evans-Yamamoto; Soh Ishiguro ; Masaru Tomita; Nozomu Yachie
 
 
A new full-length circular DNA sequencing method for viral-sized genomes reveals that RNAi transgenic plants provoke a shift in geminivirus populations in the field border= 
 
Devang Mehta ; Matthias Hirsch-Hoffmann; Mariam Were; Andrea Patrignani; Syed Shan-e-Ali Zaidi ...
 
 
Classifying cells with Scasat, a single-cell ATAC-seq analysis tool border=  
 
Syed Murtuza Baker; Connor Rogerson; Andrew Hayes ; Andrew D Sharrocks; Magnus Rattray
 
 
BiFET: sequencing Bias-free transcription factor Footprint Enrichment T est border= 
 
Ahrim Youn; Eladio J Marquez ; Nathan Lawlor; Michael L Stitzel; Duygu Ucar
 
 
Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples border= 
 
Simon Haile ; Richard D Corbett; Steve Bilobram; Morgan H Bye; Heather Kirk ...
 
 
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