Subject: Nucleic Acids Research Table of Contents for 17 March 2017 Oxford Academic
 
 
 
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New issue alert
 
Nucleic Acids Research  
Volume 45 Issue 5
 
17 March 2017
 
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NAR Breakthrough Article
 
 
 
Structured and disordered regions cooperatively mediate DNA-binding autoinhibition of ETS factors ETV1, ETV4 and ETV5 border=  
 
Simon L. Currie; Desmond K. W. Lau ; Jedediah J. Doane; Frank G. Whitby; Mark Okon ...
 
 
SURVEY AND SUMMARY
 
 
 
Genome maintenance in Saccharomyces cerevisiae: the role of SUMO and SUMO-targeted ubiquitin ligases border=  
 
Deena Jalal; Jisha Chalissery ; Ahmed H. Hassan
 
 
Managing the sequence-specificity of antisense oligonucleotides in drug discovery border=  
 
Peter H. Hagedorn; Bo R. Hansen ; Troels Koch; Morten Lindow
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Reversible manipulation of the G-quadruplex structures and enzymatic reactions through supramolecular host'guest interactions border=  
 
Tian Tian; Yanyan Song ; Lai Wei; Jiaqi Wang; Boshi Fu ...
 
 
Characterizing the effect of GalNAc and phosphorothioate backbone on binding of antisense oligonucleotides to the asialoglycoprotein receptor border=  
 
Karsten Schmidt; Thazha P. Prakash ; Aaron J. Donner; Garth A. Kinberger; Hans J. Gaus ...
 
 
 
 
Computational Biology
 
 
 
Quantifying deleterious effects of regulatory variants   
 
Shan Li; Roberto Vera Alvarez ; Roded Sharan; David Landsman; Ivan Ovcharenko
 
 
Human population-specific gene expression and transcriptional network modification with polymorphic transposable elements border=  
 
Lu Wang; Lavanya Rishishwar ; Leonardo Mariño-Ramírez; I. King Jordan
 
 
Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III in Streptococcus pyogenes border=  
 
AnaĂŻs Le Rhun; Anne-Laure LĂ©crivain ; Johan ReimegĂĄrd; Estelle Proux-WĂ©ra; Laura Broglia ...
 
 
High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq border=  
 
Rafal Gumienny; Dominik J. Jedlinski ; Alexander Schmidt; Foivos Gypas; Georges Martin ...
 
 
Data Resources and Analyses
 
 
 
Models of global gene expression define major domains of cell type and tissue identity border=  
 
Andrew P. Hutchins; Zhongzhou Yang ; Yuhao Li; Fangfang He; Xiuling Fu ...
 
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Core binding factor (CBF) is required for Epstein-Barr virus EBNA3 proteins to regulate target gene expression border=  
 
Kostas Paschos; Quentin Bazot ; Guiyi Ho; Gillian A. Parker; Jonathan Lees ...
 
 
Chromatin binding of Gcn5 in Drosophila is largely mediated by CP190 border=  
 
Tamer Ali; Marcus KrĂĽger ; Sabin Bhuju; Michael Jarek; Marek Bartkuhn ...
 
 
MAX is an epigenetic sensor of 5-carboxylcytosine and is altered in multiple myeloma border=  
 
Dongxue Wang; Hideharu Hashimoto ; Xing Zhang; Benjamin G. Barwick; Sagar Lonial ...
 
 
PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c border=  
 
Gang Pan; Adam Ameur ; Stefan Enroth; Madhusudhan Bysani; Helena Nord ...
 
 
Competitive binding between Seryl-tRNA synthetase/YY1 complex and NFKB1 at the distal segment results in differential regulation of human vegfa promoter activity during angiogenesis border=  
 
Chuan-Yang Fu; Po-Chun Wang ; Huai-Jen Tsai
 
 
Binding of MBD proteins to DNA blocks Tet1 function thereby modulating transcriptional noise border=  
 
Anne K. Ludwig; Peng Zhang ; Florian D. Hastert; Stephanie Meyer; Cathia Rausch ...
 
 
Sub1 contacts the RNA polymerase II stalk to modulate mRNA synthesis border=  
 
Miguel Garavís; Noelia González-Polo ; Paula Allepuz-Fuster; Jaime Alegrio Louro; Carlos Fernández-Tornero ...
 
 
Folate deficiency facilitates recruitment of upstream binding factor to hot spots of DNA double-strand breaks of rRNA genes and promotes its transcription border=  
 
Qiu Xie; Caihua Li ; Xiaozhen Song; Lihua Wu; Qian Jiang ...
 
 
Temporal association of ORCA/LRWD1 to late-firing origins during G1 dictates heterochromatin replication and organization border=  
 
Yating Wang; Abid Khan ; Anna B. Marks; Owen K. Smith; Sumanprava Giri ...
 
 
Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta border=  
 
Samuel Hong; Dongxue Wang ; John R. Horton; Xing Zhang; Samuel H. Speck ...
 
 
Genome Integrity, Repair and Replication
 
 
 
And-1 coordinates with CtIP for efficient homologous recombination and DNA damage checkpoint maintenance border=  
 
Yali Chen; Hailong Liu ; Haoxing Zhang; Changqing Sun; Zhaohua Hu ...
 
 
And-1 is required for homologous recombination repair by regulating DNA end resection border=  
 
Yongming Li; Zongzhu Li ; Ruiqin Wu; Zhiyong Han; Wenge Zhu
 
 
Overlapping roles for PARP1 and PARP2 in the recruitment of endogenous XRCC1 and PNKP into oxidized chromatin border=  
 
Hana Hanzlikova; William Gittens ; Katerina Krejcikova; Zhihong Zeng; Keith W. Caldecott
 
 
Degradation of Mrc1 promotes recombination-mediated restart of stalled replication forks border=  
 
Indrajit Chaudhury; Deanna M. Koepp
 
 
Inhibiting translation elongation can aid genome duplication in Escherichia coli border=  
 
Kamila K. Myka; Michelle Hawkins ; Aisha H. Syeda; Milind K. Gupta; Caroline Meharg ...
 
 
Microhomology-mediated end joining is activated in irradiated human cells due to phosphorylation-dependent formation of the XRCC1 repair complex border=  
 
Arijit Dutta; Bradley Eckelmann ; Sanjay Adhikari; Kazi Mokim Ahmed; Shiladitya Sengupta ...
 
 
Ribonucleotide incorporation by human DNA polymerase eta impacts translesion synthesis and RNase H2 activity border=  
 
Elisa Mentegari; Emmanuele Crespan ; Laura Bavagnoli; Miroslava Kissova; Federica Bertoletti ...
 
 
Alternative lengthening of telomeres can be maintained by preferential elongation of lagging strands border=  
 
Jaewon Min; Woodring E. Wright ; Jerry W. Shay
 
 
Genomics
 
 
 
Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis border=  
 
Yafeng Zhu; Pär G. Engström ; Christian Tellgren-Roth; Charles D. Baudo; John C. Kennell ...
 
 
Molecular Biology
 
 
 
Cancer-causing mutations in the tumor suppressor PALB2 reveal a novel cancer mechanism using a hidden nuclear export signal in the WD40 repeat motif border=  
 
Joris Pauty; Anthony M. Couturier ; Amélie Rodrigue; Marie-Christine Caron; Yan Coulombe ...
 
 
In vivo evidence that eIF3 stays bound to ribosomes elongating and terminating on short upstream ORFs to promote reinitiation border=  
 
Mahabub Pasha Mohammad; Vanda Munzarová PondÄ›lĂ­ÄŤková ; Jakub Zeman; Stanislava Gunišová; Leoš Shivaya Valášek
 
 
SIRT7-dependent deacetylation of CDK9 activates RNA polymerase II transcription border=  
 
Maximilian F. Blank; Sifan Chen ; Fabian Poetz; Martina Schnölzer; Renate Voit ...
 
 
TLR4-induced NF-kappa B and MAPK signaling regulate the IL-6 mRNA stabilizing protein Arid5a border=  
 
Kishan K. Nyati; Kazuya Masuda ; Mohammad Mahabub-Uz Zaman; Praveen K. Dubey; David Millrine ...
 
 
Nucleic Acid Enzymes
 
 
 
Topoisomerase 3beta is the major topoisomerase for mRNAs and linked to neurodevelopment and mental dysfunction  
 
Muzammil Ahmad; Weiping Shen ; Wen Li; Yutong Xue; Sige Zou ...
 
 
DNA binding specificities of Escherichia coli Cas1'Cas2 integrase drive its recruitment at the CRISPR locus border=  
 
Clara Moch; Michel Fromant ; Sylvain Blanquet; Pierre Plateau
 
 
DNA flap creation by the RarA/MgsA protein of Escherichia coli border=  
 
Tyler H. Stanage; Asher N. Page ; Michael M. Cox
 
 
Revealing the role of the product metal in DNA polymerase beta catalysis  
 
Lalith Perera; Bret D. Freudenthal ; William A. Beard; Lee G. Pedersen; Samuel H. Wilson
 
 
RNA
 
 
 
Landscape of RNA polyadenylation in E. coli border=  
 
Alexandre Maes; CĂ©line Gracia ; Nicolas Innocenti; Kaiyang Zhang; Erik Aurell ...
 
 
Active 5Î" splice sites regulate the biogenesis efficiency of Arabidopsis microRNAs derived from intron-containing genes border=  
 
Katarzyna Knop; Agata Stepien ; Maria Barciszewska-Pacak; Michal Taube; Dawid Bielewicz ...
 
 
Transfer RNAs with novel cloverleaf structures border=  
 
Takahito Mukai; Oscar Vargas-Rodriguez ; Markus Englert; H. James Tripp; Natalia N. Ivanova ...
 
 
Global and cell-type specific properties of lincRNAs with ribosome occupancy border=  
 
Hongwei Wang; Yan Wang ; Shangqian Xie; Yizhi Liu; Zhi Xie
 
 
Harnessing human ADAR2 for RNA repair ' Recoding a PINK1 mutation rescues mitophagy border=  
 
Jacqueline Wettengel; Philipp Reautschnig ; Sven Geisler; Philipp J. Kahle; Thorsten Stafforst
 
 
A novel role for GSK3beta as a modulator of Drosha microprocessor activity and MicroRNA biogenesis border=  
 
Claire E. Fletcher; Jack D. Godfrey ; Akifumi Shibakawa; Martin Bushell; Charlotte L. Bevan
 
 
Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate  
 
Jun Zhang; Lauren E. Gonzalez ; Traci M. Tanaka Hall
 
 
FARNA: knowledgebase of inferred functions of non-coding RNA transcripts border=  
 
Tanvir Alam; Mahmut Uludag ; Magbubah Essack; Adil Salhi; Haitham Ashoor ...
 
 
hnRNPs and ELAVL1 cooperate with uORFs to inhibit protein translation border=  
 
Jiewen Zhang; Lijuan Kong ; Sichao Guo; Mengmeng Bu; Qian Guo ...
 
 
EF-G catalyzed translocation dynamics in the presence of ribosomal frameshifting stimulatory signals border=  
 
Hee-Kyung Kim; Ignacio Tinoco, Jr
 
 
Structural Biology
 
 
 
Toxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding border=  
 
Kirstine L. Bendtsen; Kehan Xu ; Majbritt Luckmann; Kristoffer S. Winther; Shiraz A. Shah ...
 
 
Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions border=  
 
Michael Graf; Stefan Arenz ; Paul Huter; Alexandra Dönhöfer; Jiří Nováček ...
 
 
Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase border=  
 
Aishwarya Prakash; Kedar Moharana ; Susan S. Wallace; Sylvie Doublié
 
 
Flexibility and stabilization of HgII-mediated C:T and T:T base pairs in DNA duplex border=  
 
Hehua Liu; Chen Cai ; Phensinee Haruehanroengra; Qingqing Yao; Yiqing Chen ...
 
 
Synthetic Biology and Bioengineering
 
 
 
Nucleoid and cytoplasmic localization of small RNAs in Escherichia coli border=  
 
Huanjie Sheng; Weston T. Stauffer ; Razika Hussein; Chris Lin; Han N. Lim
 
 
Corrigendum
 
 
 
Human RECQL1 participates in telomere maintenance  
 
Venkateswarlu Popuri; Joseph Hsu ; Prabhat Khadka; Kent Horvath; Yie Liu ...
 
 
GPCRdb: an information system for G protein-coupled receptors border=  
 
Vignir Isberg; Stefan Mordalski ; Christian Munk; Krzysztof Rataj; Kasper Harpsøe ...
 
 
Methods Online
 
 
 
Production of DNA minicircles less than 250 base pairs through a novel concentrated DNA circularization assay enabling minicircle design with NF-kappa B inhibition activity border=  
 
Thomas Thibault; Jeril Degrouard ; Patrick Baril; Chantal Pichon; Patrick Midoux ...
 
 
Discovery and validation of information theory-based transcription factor and cofactor binding site motifs border=  
 
Ruipeng Lu; Eliseos J. Mucaki ; Peter K. Rogan
 
 
Empower multiplex cell and tissue-specific CRISPR-mediated gene manipulation with self-cleaving ribozymes and tRNA border=  
 
Li Xu; Lixia Zhao ; Yandi Gao; Jing Xu; Renzhi Han
 
 
Integration-defective lentiviral vector mediates efficient gene editing through homology-directed repair in human embryonic stem cells border=  
 
Yebo Wang; Yingjia Wang ; Tammy Chang; He Huang; Jiing-Kuan Yee
 
 
RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods border=  
 
Aliaksei Z. Holik; Charity W. Law ; Ruijie Liu; Zeya Wang; Wenyi Wang ...
 
 
A comprehensive approach to expression of L1 loci border=  
 
Prescott Deininger; Maria E. Morales ; Travis B. White; Melody Baddoo; Dale J. Hedges ...
 
 
IDP-ASE: haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing border=  
 
Benjamin Deonovic; Yunhao Wang ; Jason Weirather; Xiu-Jie Wang; Kin Fai Au
 
 
Duplication-Insertion Recombineering: a fast and scar-free method for efficient transfer of multiple mutations in bacteria border=  
 
Joakim Näsvall; Anna Knöppel ; Dan I. Andersson
 
 
sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors border=  
 
Wenhan Chen; Alan J. Robertson ; Devika Ganesamoorthy; Lachlan J.M. Coin
 
 
A high-throughput approach to profile RNA structure border=  
 
Riccardo Delli Ponti; Stefanie Marti ; Alexandros Armaos; Gian Gaetano Tartaglia
 
 
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