Subject: Nucleic Acids Research Table of Contents for 28 September 2018 ------=_Part_902690488.1538327927527 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.mcmaster.ca. ------=_Part_902690488.1538327927527 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Nucleic Acids Research  
Volume 46 Issue 17
 
28 September 2018
 
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Survey and Summary
 
 
 
Replication-dependent histone isoforms: a new source of complexity in chromatin structure and function border= 
 
Rajbir Singh; Emily Bassett; Arnab Chakravarti; Mark R Parthun
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Modification of the aminopyridine unit of 2²-deoxyaminopyridinyl-pseudocytidine allowing triplex formation at CG interruptions in homopurine sequences border= 
 
Lei Wang ; Yosuke Taniguchi; Hidenori Okamura; Shigeki Sasaki
 
 
Chemical genetic inhibition of DEAD-box proteins using covalent complementarity border=  
 
Krister J Barkovich; Megan K Moore; Qi Hu ; Kevan M Shokat
 
 
Tunable order'disorder continuum in protein'DNA interactions border= 
 
Sneha Munshi; Soundhararajan Gopi; Gitanjali Asampille ; Sandhyaa Subramanian; Luis A Campos ...
 
 
Structural optimization of pseudorotaxane-forming oligonucleotides for efficient and stable complex formation border=  
 
Kazumitsu Onizuka; Takuya Miyashita; Tomoko Chikuni ; Mamiko Ozawa; Hiroshi Abe ...
 
 
 
Computational Biology
 
 
 
Identification of transcribed protein coding sequence remnants within lincRNAs border=  
 
Sweta Talyan; Miguel A Andrade-Navarro; Enrique M Muro
 
 
PAREsnip2: a tool for high-throughput prediction of small RNA targets from degradome sequencing data using configurable targeting rules border= 
 
Joshua Thody ; Leighton Folkes; Zahara Medina-Calzada; Ping Xu; Tamas Dalmay ...
 
 
INFERNO: inferring the molecular mechanisms of noncoding genetic variants border=  
 
Alexandre Amlie-Wolf; Mitchell Tang; Elisabeth E Mlynarski ; Pavel P Kuksa; Otto Valladares ...
 
 
Structural dynamics of propeller loop: towards folding of RNA G-quadruplex border=  
 
Marek Havrila; Petr Stadlbauer; Petra Kührová ; Pavel BanáÅ¡; Jean-Louis Mergny ...
 
 
 
Data Resources and Analyses
 
 
 
The Xenopus animal cap transcriptome: building a mucociliary epithelium border=  
 
Alessandro Angerilli; Pawel Smialowski; Ralph AW Rupp
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
KAP1 facilitates reinstatement of heterochromatin after DNA replication border=  
 
Suk Min Jang; Annamaria Kauzlaric; Jean-Pierre Quivy ; Julien Pontis; Benjamin Rauwel ...
 
 
The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus border=  
 
Tatiana Rochat; Chantal Bohn; Claire Morvan ; Thao Nguyen Le Lam; Fareha Razvi ...
 
 
H2A.Z.1 crosstalk with H3K56-acetylation controls gliogenesis through the transcription of folate receptor border=  
 
Libo Su; Wenlong Xia; Tianjin Shen ; Qingli Liang; Wenwen Wang ...
 
 
Loss of tumor suppressor IGFBP4 drives epigenetic reprogramming in hepatic carcinogenesis border=  
 
Ying-Ying Lee; Myth TS Mok; Wei Kang ; Weiqin Yang; Wenshu Tang ...
 
 
Three classes of response elements for human PRC2 and MLL1/2'Trithorax complexes border=  
 
Junqing Du; Brian Kirk; Jia Zeng ; Jianpeng Ma; Qinghua Wang
 
 
Fission yeast telosomes: non-canonical histone-containing chromatin structures dependent on shelterin and RNA 
 
Jessica Greenwood; Harshil Patel; Thomas R Cech; Julia Promisel Cooper
 
 
VpsR and cyclic di-GMP together drive transcription initiation to activate biofilm formation in Vibrio cholerae  border= 
 
Meng-Lun Hsieh; Deborah M Hinton ; Christopher M Waters
 
 
Genome wide analyses uncover allele-specific RNA editing in human and mouse border=  
 
Zhong-Yin Zhou; Yue Hu; Aimin Li ; Ying-Ju Li; Hui Zhao ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
Loss of E2F7 confers resistance to poly-ADP-ribose polymerase (PARP) inhibitors in BRCA2-deficient cells border= 
 
Kristen E Clements; Tanay Thakar; Claudia M Nicolae; Xinwen Liang; Hong-Gang Wang ...
 
 
PARP10 promotes cellular proliferation and tumorigenesis by alleviating replication stress border=  
 
Emily M Schleicher; Adri M Galvan; Yuka Imamura-Kawasawa ; George-Lucian Moldovan; Claudia M Nicolae
 
 
The 2B subdomain of Rep helicase links translocation along DNA with protein displacement border=  
 
Jan-Gert Brüning; Jamieson A L Howard; Kamila K Myka ; Mark S Dillingham; Peter McGlynn
 
 
TDP1 suppresses mis-joining of radiomimetic DNA double-strand breaks and cooperates with Artemis to promote optimal nonhomologous end joining border= 
 
Ajinkya S Kawale ; Konstantin Akopiants; Kristoffer Valerie; Brian Ruis; Eric A Hendrickson ...
 
 
The deoxyribose phosphate lyase of DNA polymerase beta suppresses a processive DNA synthesis to prevent trinucleotide repeat instability border= 
 
Yanhao Lai ; Yossi Weizmann; Yuan Liu
 
 
 
Genomics
 
 
 
Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats border= 
 
Michael Schmid; Daniel Frei ; Andrea Patrignani; Ralph Schlapbach; Jürg E Frey ...
 
 
 
Molecular Biology
 
 
 
Protein encoded in human telomerase RNA is involved in cell protective pathways border= 
 
Maria Rubtsova; Yulia Naraykina ; Daria Vasilkova; Mark Meerson; Maria Zvereva ...
 
 
Polymorphism of G4 associates: from stacks to wires via interlocks border= 
 
Anna M Varizhuk; Anna D Protopopova; Vladimir B Tsvetkov ; Nikolay A Barinov; Victor V Podgorsky ...
 
 
The suppressive cap-binding complex factor 4EIP is required for normal differentiation border=  
 
Monica Terrao; Kevin K Marucha; Elisha Mugo ; Dorothea Droll; Igor Minia ...
 
 
A DNA-sensing'independent role of a nuclear RNA helicase, DHX9, in stimulation of NF-kappa B'mediated innate immunity against DNA virus infection border= 
 
Yee Ching Ng ; Woo-Chang Chung; Hye-Ri Kang; Hye-Jeong Cho; Eun-Byeol Park ...
 
 
 
Nucleic Acid Enzymes
 
 
 
The trimeric Hef-associated nuclease HAN is a 3²â†'5² exonuclease and is probably involved in DNA repair border= 
 
Lei Feng; Chen-Chen Chang ; Dong Song; Chuang Jiang; Yang Song ...
 
 
Chromatin-dependent allosteric regulation of DNMT3A activity by MeCP2 border=  
 
Arumugam Rajavelu; Cristiana Lungu; Max Emperle ; Michael Dukatz; Alexander Bröhm ...
 
 
Structure-specific endonuclease activity of SNM1A enables processing of a DNA interstrand crosslink border=  
 
Beverlee Buzon; Ryan Grainger; Simon Huang ; Cameron Rzadki; Murray S Junop
 
 
A model for the evolution of prokaryotic DNA restriction-modification systems based upon the structural malleability of Type I restriction-modification enzymes border= 
 
Edward K M Bower ; Laurie P Cooper; Gareth A Roberts; John H White; Yvette Luyten ...
 
 
 
RNA and RNA-protein complexes
 
 
 
Dimerization confers increased stability to nucleases in 5² halves from glycine and glutamic acid tRNAs border= 
 
Juan Pablo Tosar; Fabiana Gámbaro; Leonardo Darré; Sergio Pantano; Eric Westhof ...
 
 
A functional genetic screen reveals sequence preferences within a key tertiary interaction in cobalamin riboswitches required for ligand selectivity border= 
 
Jacob T Polaski ; Otto A Kletzien; Lea K Drogalis; Robert T Batey
 
 
SOX9 has distinct regulatory roles in alternative splicing and transcription border=  
 
Michael Girardot; Elsa Bayet; Justine Maurin ; Philippe Fort; Pierre Roux ...
 
 
MBNL splicing activity depends on RNA binding site structural context border=  
 
Katarzyna Taylor; Å ukasz J Sznajder; Piotr Cywoniuk ; James D Thomas; Maurice S Swanson ...
 
 
LGP2 virus sensor regulates gene expression network mediated by TRBP-bound microRNAs border=  
 
Tomoko Takahashi; Yuko Nakano; Koji Onomoto ; Fuminori Murakami; Chiaki Komori ...
 
 
SMA1, a homolog of the splicing factor Prp28, has a multifaceted role in miRNA biogenesis in Arabidopsis border=  
 
Shengjun Li; Ran Xu; Aixia Li ; Kan Liu; Liqing Gu ...
 
 
Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine border=  
 
Huijeong Ryu; Tyler L Grove; Steven C Almo ; Jungwook Kim
 
 
Small but large enough: structural properties of armless mitochondrial tRNAs from the nematode Romanomermis culicivorax  border= 
 
Tina Jühling; Elke Duchardt-Ferner ; Sonja Bonin; Jens Wöhnert; Joern Pütz ...
 
 
 
Structural Biology
 
 
 
Two convergent pathways of DNA knotting in replicating DNA molecules as revealed by theta -curve analysis border= 
 
Danielle O'Donnol; Andrzej Stasiak; Dorothy Buck
 
 
Nucleosome conformational variability in solution and in interphase nuclei evidenced by cryo-electron microscopy of vitreous sections border= 
 
Mikhail Eltsov ; Diana Grewe; Nicolas Lemercier; Achilleas Frangakis; Françoise Livolant ...
 
 
TraN: A novel repressor of an Enterococcus conjugative type IV secretion system border=  
 
Verena Kohler; Nikolaus Goessweiner-Mohr; Andreas Aufschnaiter ; Christian Fercher; Ines Probst ...
 
 
TGIF1 homeodomain interacts with Smad MH1 domain and represses TGF-beta signaling border=  
 
Ewelina Guca; David Suñol; Lidia Ruiz ; Agnieszka Konkol; Jorge Cordero ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
Directed evolution of Escherichia coli with lower-than-natural plasmid mutation rates border= 
 
Daniel E Deatherage; Dacia Leon ; Álvaro E Rodriguez; Salma K Omar; Jeffrey E Barrick
 
 
 
Corrigendum
 
 
 
Bio-TDS: bioscience query tool discovery system border=  
 
Etienne Z Gnimpieba; Menno S VanDiermen; Shayla M Gustafson ; Bill Conn; Carol M Lushbough
 
 
 
Erratum
 
 
 
Optimized knock-in of point mutations in zebrafish using CRISPR/Cas9 border=  
 
Sergey V Prykhozhij; Charlotte Fuller; Shelby L Steele ; Chansey J Veinotte; Babak Razaghi ...
 
 
 
Methods Online
 
 
 
CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci border= 
 
Ipek Tasan; Gabriela Sustackova; Liguo Zhang; Jiah Kim; Mayandi Sivaguru ...
 
 
qEva-CRISPR: a method for quantitative evaluation of CRISPR/Cas-mediated genome editing in target and off-target sites border= 
 
Magdalena Dabrowska ; Karol Czubak; Wojciech Juzwa; Wlodzimierz J Krzyzosiak; Marta Olejniczak ...
 
 
Optimized knock-in of point mutations in zebrafish using CRISPR/Cas9 border=  
 
Sergey V Prykhozhij; Charlotte Fuller; Shelby L Steele ; Chansey J Veinotte; Babak Razaghi ...
 
 
3²-End labeling of nucleic acids by a polymerase ribozyme border= 
 
Biswajit Samanta; David P Horning; Gerald F Joyce
 
 
Animal Hen1 2²-O-methyltransferases as tools for 3²-terminal functionalization and labelling of single-stranded RNAs border=  
 
Milda MickutÄ-; Milda NainytÄ-; Lina VasiliauskaitÄ- ; Alexandra Plotnikova; Viktoras Masevičius ...
 
 
Highly efficient RNAi and Cas9-based auto-cloning systems for C. elegans research border=  
 
Ádám Sturm; Éva SaskÅ'i; Kovács Tibor ; Nóra Weinhardt; Tibor Vellai
 
 
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