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 ------=_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
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
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
Bio-TDS: bioscience query tool discovery system border=  
Etienne Z Gnimpieba; Menno S VanDiermen; Shayla M Gustafson ; Bill Conn; Carol M Lushbough
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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