Subject: Nucleic Acids Research Table of Contents for 20 June 2018 ------=_Part_1365850721.1529775010233 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1365850721.1529775010233 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Nucleic Acids Research  
Volume 46 Issue 11
 
20 June 2018
 
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Chemical Biology and Nucleic Acid Chemistry
 
 
 
Mechanistic alternatives for peptide bond formation on the ribosome border= 
 
Masoud Kazemi; Jaka Sočan; Fahmi Himo; Johan Åqvist
 
 
Cell penetrating thiazole peptides inhibit c-MYC expression via site-specific targeting of c-MYC G-quadruplex border= 
 
Debasish Dutta ; Manish Debnath; Diana Müller; Rakesh Paul; Tania Das ...
 
 
Identifying and avoiding off-target effects of RNase H-dependent antisense oligonucleotides in mice border= 
 
Peter H Hagedorn; Malene Pontoppidan; Tina S Bisgaard; Marco Berrera; Andreas Dieckmann ...
 
 
Computational Biology
 
 
 
bpRNA: large-scale automated annotation and analysis of RNA secondary structure border= 
 
Padideh Danaee; Mason Rouches; Michelle Wiley; Dezhong Deng ; Liang Huang ...
 
 
Towards a map of cis-regulatory sequences in the human genome border= 
 
Meng Niu; Ehsan Tabari; Pengyu Ni; Zhengchang Su
 
 
Base-flipping dynamics from an intrahelical to an extrahelical state exerted by thymine DNA glycosylase during DNA repair process border= 
 
Lin-Tai Da ; Jin Yu
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Histone deacetylation promotes transcriptional silencing at facultative heterochromatin border= 
 
Beth R Watts ; Sina Wittmann; Maxime Wery; Camille Gautier; Krzysztof Kus ...
 
 
LSD1 mediates metabolic reprogramming by glucocorticoids during myogenic differentiation border= 
 
Kotaro Anan; Shinjiro Hino ; Noriaki Shimizu; Akihisa Sakamoto; Katsuya Nagaoka ...
 
 
Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities border=  
 
Sarah Rennie; Maria Dalby; Marta Lloret-Llinares ; Stylianos Bakoulis; Christian Dalager Vaagensø ...
 
 
DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1 border= 
 
Xuecong Wang; Yogesh Srivastava; Aleksander Jankowski; Vikas Malik ; Yuanjie Wei ...
 
 
Widespread enhancer activation via ERalpha mediates estrogen response in vivo during uterine development 
 
Wendy N Jefferson ; H Karimi Kinyamu; Tianyuan Wang; Adam X Miranda; Elizabeth Padilla-Banks ...
 
 
A novel long non-coding RNA from NBL2 pericentromeric macrosatellite forms a perinucleolar aggregate structure in colon cancer border= 
 
Gabrijela Dumbović ; Josep Biayna; Jordi Banús; Johanna Samuelsson; Anna Roth ...
 
 
StpA and Hha stimulate pausing by RNA polymerase by promoting DNA'DNA bridging of H-NS filaments border= 
 
Beth A Boudreau; Daniel R Hron ; Liang Qin; Ramon A van der Valk; Matthew V Kotlajich ...
 
 
The KDM4A/KDM4C/NF-kappa B and WDR5 epigenetic cascade regulates the activation of B cells border= 
 
Kuo-Hsuan Hung; Yong H Woo; I-Ying Lin ; Chin-Hsiu Liu; Li-Chieh Wang ...
 
 
Emerin modulates spatial organization of chromosome territories in cells on softer matrices border= 
 
Roopali Pradhan; Devika Ranade; Kundan Sengupta
 
 
The longevity SNP rs2802292 uncovered: HSF1 activates stress-dependent expression of FOXO3 through an intronic enhancer border= 
 
Valentina Grossi ; Giovanna Forte; Paola Sanese; Alessia Peserico; Tugsan Tezil ...
 
 
Genome Integrity, Repair and Replication
 
 
 
PRMT5-mediated arginine methylation of TDP1 for the repair of topoisomerase I covalent complexes border=  
 
Ishita Rehman; Suparna M Basu; Subhendu K Das ; Sangheeta Bhattacharjee; Arijit Ghosh ...
 
 
Regional conformational flexibility couples substrate specificity and scissile phosphate diester selectivity in human flap endonuclease 1 border= 
 
Ian A Bennet; L David Finger; Nicola J Baxter; Benjamin Ambrose ; Andrea M Hounslow ...
 
 
Flap endonuclease overexpression drives genome instability and DNA damage hypersensitivity in a PCNA-dependent manner border= 
 
Jordan R Becker; David Gallo; Wendy Leung; Taylor Croissant; Yee Mon Thu ...
 
 
Physical and functional interplay between PCNA DNA clamp and Mre11'Rad50 complex from the archaeon Pyrococcus furiosus border= 
 
Gaëlle Hogrel; Yang Lu; Sébastien Laurent; Etienne Henry; Clarisse Etienne ...
 
 
APE1 deficiency promotes cellular senescence and premature aging features  
 
Mengxia Li; Xiao Yang; Xianfeng Lu ; Nan Dai; Shiheng Zhang ...
 
 
Genomics
 
 
 
Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species border= 
 
Lauren M Lui; Andrew V Uzilov; David L Bernick; Andrea Corredor ; Todd M Lowe ...
 
 
Translational control plays an important role in the adaptive heat-shock response of Streptomyces coelicolor border= 
 
Giselda Bucca; Radhika Pothi; Andrew Hesketh; Carla Möller-Levet; David A Hodgson ...
 
 
Molecular Biology
 
 
 
The TubR'centromere complex adopts a double-ring segrosome structure in Type III partition systems border= 
 
Bárbara Martín-García ; Alejandro Martín-González; Carolina Carrasco; Ana M Hernández-Arriaga; Rubén Ruíz-Quero ...
 
 
Modulation of H-NS transcriptional silencing by magnesium border= 
 
W Ryan Will; Patrick J Whitham ; Philip J Reid; Ferric C Fang
 
 
Nucleic Acid Enzymes
 
 
 
Microprocessor depends on hemin to recognize the apical loop of primary microRNA border= 
 
Tuan Anh Nguyen; Joha Park; Thi Lieu Dang; Yeon-Gil Choi; V Narry Kim
 
 
Dicer cleaves 5²-extended microRNA precursors originating from RNA polymerase II transcription start sites border= 
 
Peike Sheng ; Christopher Fields; Kelsey Aadland; Tianqi Wei; Oralia Kolaczkowski ...
 
 
Base modifications affecting RNA polymerase and reverse transcriptase fidelity border= 
 
Vladimir Potapov; Xiaoqing Fu ; Nan Dai; Ivan R Corrêa, Jr; Nathan A Tanner ...
 
 
RNA'DNA and DNA'DNA base-pairing at the upstream edge of the transcription bubble regulate translocation of RNA polymerase and transcription rate 
 
Maria KIreeva; Cyndi Trang; Gayane Matevosyan; Joshua Turek-Herman ; Vitaly Chasov ...
 
 
RNA and RNA-protein complexes
 
 
 
Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection border= 
 
Will McIntyre; Rachel Netzband; Gaston Bonenfant; Jason M Biegel; Clare Miller ...
 
 
4EHP-independent repression of endogenous mRNAs by the RNA-binding protein GIGYF2 border= 
 
Cinthia C Amaya Ramirez; Petra Hubbe ; Nicolas Mandel; Julien Béthune
 
 
Long noncoding RNA OCC-1 suppresses cell growth through destabilizing HuR protein in colorectal cancer border= 
 
Yang Lan; Xuewei Xiao; Zhengchi He; Yu Luo ; Chuanfang Wu ...
 
 
The loss of SMG1 causes defects in quality control pathways in Physcomitrella patens border= 
 
James P B Lloyd; Daniel Lang; Andreas D Zimmer; Barry Causier; Ralf Reski ...
 
 
Cell-wall synthesis and ribosome maturation are co-regulated by an RNA switch in Mycobacterium tuberculosis border= 
 
Stefan Schwenk ; Alexandra Moores; Irene Nobeli; Timothy D McHugh; Kristine B Arnvig
 
 
Structural Biology
 
 
 
The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification border=  
 
Sophia Missoury; Stéphane Plancqueel; Ines Li de la Sierra-Gallay ; Wenhua Zhang; Dominique Liger ...
 
 
Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A border= 
 
Marcus Fislage; Jingji Zhang; Zuben Patrick Brown; Chandra Sekhar Mandava ; Suparna Sanyal ...
 
 
Methods Online
 
 
 
A general strategy for direct, enzyme-catalyzed conjugation of functional compounds to DNA border= 
 
Jochem Deen ; Su Wang; Sven Van Snick; Volker Leen; Kris Janssen ...
 
 
Post-transcriptional labeling by using Suzuki'Miyaura cross-coupling generates functional RNA probes border= 
 
Manisha B Walunj; Arun A Tanpure; Seergazhi G Srivatsan
 
 
Simultaneous determination of ribonucleoside and deoxyribonucleoside triphosphates in biological samples by hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry border= 
 
Ziqing Kong; Shaodong Jia; Anna Lena Chabes; Patrik Appelblad ; Richard Lundmark ...
 
 
TGMI: an efficient algorithm for identifying pathway regulators through evaluation of triple-gene mutual interaction border= 
 
Chathura Gunasekara; Kui Zhang; Wenping Deng; Laura Brown; Hairong Wei
 
 
riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions border= 
 
Nicholas R Waters ; Florence Abram; Fiona Brennan; Ashleigh Holmes; Leighton Pritchard
 
 
DeFine: deep convolutional neural networks accurately quantify intensities of transcription factor-DNA binding and facilitate evaluation of functional non-coding variants border= 
 
Meng Wang ; Cheng Tai; Weinan E; Liping Wei
 
 
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