Subject: Nucleic Acids Research Table of Contents for 20 June 2017 Oxford Academic
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Nucleic Acids Research  
Volume 45 Issue 11
20 June 2017
Mass spectrometry for serine ADP-ribosylation? Think o-glycosylation! border= 
Juan J. Bonfiglio; Thomas Colby; Ivan Matic
Chemical Biology and Nucleic Acid Chemistry
Ball with hair: modular functionalization of highly stable G-quadruplex DNA nano-scaffolds through N2-guanine modification border= 
Christopher Jacques Lech ; Anh Tuân Phan
Interstrand cross-links arising from strand breaks at true abasic sites in duplex DNA border= 
Zhiyu Yang; Nathan E. Price; Kevin M. Johnson; Yinsheng Wang; Kent S. Gates
Computational Biology
Structure and conformational dynamics of scaffolded DNA origami nanoparticles border= 
Keyao Pan ; William P. Bricker; Sakul Ratanalert; Mark Bathe
Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide'nucleotide interactions from direct coupling analysis border=  
Jian Wang; Kangkun Mao; Yunjie Zhao ; Chen Zeng; Jianjin Xiang ...
Data Resources and Analyses
A new model for ancient DNA decay based on paleogenomic meta-analysis border= 
Logan Kistler; Roselyn Ware; Oliver Smith; Matthew Collins ; Robin G. Allaby
Gene Regulation, Chromatin and Epigenetics
Heat shock factor 1 promotes TERRA transcription and telomere protection upon heat stress border= 
Sivan Koskas; Anabelle Decottignies; Solenne Dufour; Mylène Pezet; André Verdel ...
Histone deacetylase class-I inhibition promotes epithelial gene expression in pancreatic cancer cells in a BRD4- and MYC-dependent manner border= 
Vivek Kumar Mishra; Florian Wegwitz; Robyn Laura Kosinsky; Madhobi Sen; Roland Baumgartner ...
The haploinsufficient tumor suppressor, CUX1, acts as an analog transcriptional regulator that controls target genes through distal enhancers that loop to target promoters border= 
Robert K. Arthur ; Ningfei An; Saira Khan; Megan E. McNerney
The elongation factor Spt4/5 regulates RNA polymerase II transcription through the nucleosome border= 
John B. Crickard; Jaehyoun Lee; Tae-Hee Lee; Joseph C. Reese
Molecular basis for the methylation specificity of ATXR5 for histone H3 border= 
Elisa Bergamin; Sabina Sarvan ; Josée Malette; Mohammad S. Eram; Sylvain Yeung ...
MLL3/MLL4 are required for CBP/p300 binding on enhancers and super-enhancer formation in brown adipogenesis 
Binbin Lai; Ji-Eun Lee; Younghoon Jang; Lifeng Wang ; Weiqun Peng ...
The LSH/HELLS homolog Irc5 contributes to cohesin association with chromatin in yeast border= 
Ireneusz Litwin; Tomasz Bakowski; Ewa Maciaszczyk-Dziubinska; Robert Wysocki
Bidirectional terminators in Saccharomyces cerevisiae prevent cryptic transcription from invading neighboring genes border= 
Nicole Uwimana; Pierre Collin ; Célia Jeronimo; Benjamin Haibe-Kains; François Robert
H3K4 demethylase KDM5B regulates global dynamics of transcription elongation and alternative splicing in embryonic stem cells border= 
Runsheng He; Benjamin L. Kidder
BRG1 interacts with SOX10 to establish the melanocyte lineage and to promote differentiation border= 
Himangi G. Marathe; Dawn E. Watkins-Chow ; Matthias Weider; Alana Hoffmann; Gaurav Mehta ...
A new promoter element associated with daily time keeping in Drosophila border= 
Brandi Sharp; Eric Paquet; Felix Naef; Akanksha Bafna ; Herman Wijnen
Genome Integrity, Repair and Replication
SeqA structures behind Escherichia coli replication forks affect replication elongation and restart mechanisms border= 
Ida Benedikte Pedersen; Emily Helgesen; Ingvild Flåtten; Solveig Fossum-Raunehaug; Kirsten Skarstad
Replication and repair of a reduced 2"-deoxyguanosine-abasic site interstrand cross-link in human cells border= 
Nathan E. Price ; Lin Li; Kent S. Gates; Yinsheng Wang
Potent DNA strand annealing activity associated with mouse Mcm2∼7 heterohexameric complex border= 
Zhiying You; Hisao Masai
Sak and Sak4 recombinases are required for bacteriophage replication in Staphylococcus aureus border=  
Maan M. Neamah; Ignacio Mir-Sanchis; María López-Sanz ; Sonia Acosta; Ignacio Baquedano ...
Transcriptional mutagenesis reduces splicing fidelity in mammalian cells border= 
Joao A. Paredes; Monika Ezerskyte; Matteo Bottai; Kristian Dreij
The RNA binding protein Npl3 promotes resection of DNA double-strand breaks by regulating the levels of Exo1 border= 
Chiara Vittoria Colombo; Camilla Trovesi; Luca Menin; Maria Pia Longhese; Michela Clerici
PRL-3 promotes telomere deprotection and chromosomal instability border= 
Shenyi Lian; Lin Meng; Yongyong Yang; Ting Ma ; Xiaofang Xing ...
Krüppel-like factors compete for promoters and enhancers to fine-tune transcription border= 
Melissa D. Ilsley; Kevin R. Gillinder; Graham W. Magor; Stephen Huang; Timothy L. Bailey ...
Molecular Biology
Strong transcription blockage mediated by R-loop formation within a G-rich homopurine'homopyrimidine sequence localized in the vicinity of the promoter border= 
Boris P. Belotserkovskii; Jane Hae Soo Shin; Philip C. Hanawalt
Cmr is a redox-responsive regulator of DosR that contributes to M. tuberculosis virulence border= 
Laura J. Smith; Aleksandra Bochkareva; Matthew D. Rolfe; Debbie M. Hunt; Christina Kahramanoglou ...
Phosphorylation of the transcriptional repressor MYB15 by mitogen-activated protein kinase 6 is required for freezing tolerance in Arabidopsis border= 
Sun Ho Kim; Ho Soo Kim; Sunghwa Bahk; Jonguk An; Yeji Yoo ...
The DEAD-box helicase Mss116 plays distinct roles in mitochondrial ribogenesis and mRNA-specific translation border= 
Dasmanthie De Silva ; Sarah Poliquin; Rui Zeng; Angelica Zamudio-Ochoa; Natalie Marrero ...
Nucleic Acid Enzymes
Transposition of Mutator'like transposable elements (MULEs) resembles hAT and Transib elements and V(D)J recombination border= 
Kun Liu; Susan R. Wessler
Human DDX21 binds and unwinds RNA guanine quadruplexes border= 
Ewan K.S. McRae ; Evan P. Booy; Aniel Moya-Torres; Peyman Ezzati; Jörg Stetefeld ...
Mechanism of bacterial gene rearrangement: SprA-catalyzed precise DNA recombination and its directionality control by SprB ensure the gene rearrangement and stable expression of spsM during sporulation in Bacillus subtilis border= 
Kimihiro Abe ; Takuo Takamatsu; Tsutomu Sato
Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6 border= 
Ru-Juan Liu; Tao Long; Jing Li; Hao Li ; En-Duo Wang
CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion border= 
Jerry F. Tien; Alborz Mazloomian; S.-W. Grace Cheng; Christopher S. Hughes; Christalle C.T. Chow ...
Critical 23S rRNA interactions for macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain border= 
Miriam Koch ; Jessica Willi; Ugo Pradère; Jonathan Hall; Norbert Polacek
SUMO conjugation to spliceosomal proteins is required for efficient pre-mRNA splicing border= 
Berta Pozzi; Laureano Bragado ; Cindy L. Will; Pablo Mammi; Guillermo Risso ...
The RNA targetome of Staphylococcus aureus non-coding RNA RsaA: impact on cell surface properties and defense mechanisms border= 
Arnaud Tomasini; Karen Moreau; Johana Chicher ; Thomas Geissmann; François Vandenesch ...
An RRM'ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion border= 
Katherine M. Collins; Yaroslav A. Kainov; Evangelos Christodolou; Debashish Ray ; Quaid Morris ...
Identification and dynamic changes of RNAs isolated from RALY-containing ribonucleoprotein complexes border= 
Annalisa Rossi; Albertomaria Moro; Toma Tebaldi; Nicola Cornella; Lisa Gasperini ...
Essential role for non-canonical poly(A) polymerase GLD4 in cytoplasmic polyadenylation and carbohydrate metabolism border= 
Jihae Shin ; Ki Young Paek; Maria Ivshina; Emily E. Stackpole; Joel D. Richter
Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA: a structural scaffold for nuclear, cytoplasmic and viral proteins  
Joanna Sztuba-Solinska; Jason W. Rausch; Rodman Smith ; Jennifer T. Miller; Denise Whitby ...
Poly(A)-specific ribonuclease is a nuclear ribosome biogenesis factor involved in human 18S rRNA maturation border= 
Christian Montellese; Nathalie Montel-Lehry; Anthony K. Henras; Ulrike Kutay ; Pierre-Emmanuel Gleizes ...
Stepwise assembly of the earliest precursors of large ribosomal subunits in yeast border= 
Wu Chen; Zhensheng Xie; Fuquan Yang; Keqiong Ye
Nonsense-mediated mRNA decay in Tetrahymena is EJC independent and requires a protozoa-specific nuclease border= 
Miao Tian; Wentao Yang ; Jing Zhang; Huai Dang; Xingyi Lu ...
Reconstitution of a functional 7SK snRNP border= 
John E. Brogie; David H. Price
The non-stop decay mRNA surveillance pathway is required for oxidative stress tolerance border= 
Nur H. Jamar; Paraskevi Kritsiligkou; Chris M. Grant
WIG1 is crucial for AGO2-mediated ACOT7 mRNA silencing via miRNA-dependent and -independent mechanisms border= 
Hyung Chul Lee; Seung Hee Jung ; Hyun Jung Hwang; Donghee Kang; Supriyo De ...
A synergistic network of interactions promotes the formation of in vitro processing bodies and protects mRNA against decapping border=  
Stefan Schütz; Erik R. Nöldeke; Remco Sprangers
Structural Biology
The Streptomyces master regulator BldD binds c-di-GMP sequentially to create a functional BldD2-(c-di-GMP)4 complex border= 
Maria A. Schumacher ; Wenjie Zeng; Kim C. Findlay; Mark J. Buttner; Richard G. Brennan ...
Capturing a mammalian DNA polymerase extending from an oxidized nucleotide border= 
Amy M. Whitaker; Mallory R. Smith ; Matthew A. Schaich; Bret D. Freudenthal
RsgA couples the maturation state of the 30S ribosomal decoding center to activation of its GTPase pocket border= 
Jorge Pedro López-Alonso; Tatsuya Kaminishi; Takeshi Kikuchi; Yuya Hirata ; Idoia Iturrioz ...
The effect of increasing numbers of repeats on TAL effector DNA binding specificity border= 
Fabio C. Rinaldi; Lindsey A. Doyle; Barry L. Stoddard; Adam J. Bogdanove
Synthetic Biology and Bioengineering
Large-scale recoding of a bacterial genome by iterative recombineering of synthetic DNA border= 
Yu Heng Lau; Finn Stirling ; James Kuo; Michiel A. P. Karrenbelt; Yujia A. Chan ...
Translation initiation events on structured eukaryotic mRNAs generate gene expression noise border= 
Estelle Dacheux; Naglis Malys; Xiang Meng; Vinoy Ramachandran ; Pedro Mendes ...
Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence border= 
Benjamin Sunkel; Dayong Wu; Zhong Chen; Chiou-Miin Wang; Xiangtao Liu ...
Identification of metabolically stable 5"-phosphate analogs that support single-stranded siRNA activity border= 
Thazha P. Prakash ; Walt F. Lima; Heather M. Murray; Wenyu Li; Garth A. Kinberger ...
Methods Online
Statistical analysis of genetic interactions in Tn-Seq data border= 
Michael A. DeJesus; Subhalaxmi Nambi ; Clare M. Smith; Richard E. Baker; Christopher M. Sassetti ...
Twin-primer non-enzymatic DNA assembly: an efficient and accurate multi-part DNA assembly method border= 
Jing Liang; Zihe Liu; Xi Z. Low; Ee L. Ang ; Huimin Zhao
Defining the 5" and 3" landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq border= 
Shaked Afik; Osnat Bartok; Maxim N. Artyomov; Alexander A. Shishkin; Sabah Kadri ...
APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins border= 
Malvika Sharan ; Konrad U. Förstner; Ana Eulalio; Jörg Vogel
Enrichment methods provide a feasible approach to comprehensive and adequately powered investigations of the brain methylome border= 
Robin F. Chan; Andrey A. Shabalin; Lin Y. Xie ; Daniel E. Adkins; Min Zhao ...
Targeted gene knock-in by homology-directed genome editing using Cas9 ribonucleoprotein and AAV donor delivery border= 
Thomas Gaj; Brett T. Staahl; Gonçalo M. C. Rodrigues; Prajit Limsirichai ; Freja K. Ekman ...
Predicting the impact of non-coding variants on DNA methylation border= 
Haoyang Zeng; David K. Gifford
PosiGene: automated and easy-to-use pipeline for genome-wide detection of positively selected genes border= 
Arne Sahm; Martin Bens; Matthias Platzer; Karol Szafranski
Flexible CRISPR library construction using parallel oligonucleotide retrieval 
Abigail Read; Shaojian Gao; Eric Batchelor ; Ji Luo
A platform for functional assessment of large variant libraries in mammalian cells border= 
Kenneth A. Matreyek; Jason J. Stephany; Douglas M. Fowler
NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types border= 
Sejoon Lee; Soohyun Lee; Scott Ouellette; Woong-Yang Park; Eunjung A. Lee ...
Modeling bias and variation in the stochastic processes of small RNA sequencing border= 
Christos Argyropoulos; Alton Etheridge; Nikita Sakhanenko; David Galas
Orientation-dependent FRET system reveals differences in structures and flexibilities of nicked and gapped DNA duplexes border= 
Hiromu Kashida; Ayako Kurihara; Hayato Kawai; Hiroyuki Asanuma
Differential expression analysis for RNAseq using Poisson mixed models border= 
Shiquan Sun; Michelle Hood; Laura Scott; Qinke Peng ; Sayan Mukherjee ...
A novel excision selection method for isolation of antibodies binding antigens expressed specifically by rare cells in tissue sections border= 
Simon Lykkemark; Ole Aalund Mandrup; Mads Bjørnkjær Jensen; Jesper Just; Peter Kristensen
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