Subject: Nucleic Acids Research Table of Contents for 6 September 2017 Oxford Academic
 
 
 
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New issue alert
 
Nucleic Acids Research  
Volume 45 Issue 15
 
6 September 2017
 
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NAR Breakthrough Article
 
 
 
A snoRNA modulates mRNA 3≤ end processing and regulates the expression of a subset of mRNAs border= 
 
Chunliu Huang; Junjie Shi; Yibin Guo; Weijun Huang ; Shanshan Huang ...
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
mRNA cap analogues substituted in the tetraphosphate chain with CX2: identification of O-to-CCl2 as the first bridging modification that confers resistance to decapping without impairing translation border= 
 
Anna M. Rydzik; Marcin Warminski; Pawel J. Sikorski; Marek R. Baranowski ; Sylwia Walczak ...
 
 
Selective tumor cell death induced by irradiated riboflavin through recognizing DNA G'T mismatch border= 
 
Yi Yuan; Yongyun Zhao; Lianqi Chen; Jiasi Wu; Gangyi Chen ...
 
 
Multimerization rules for G-quadruplexes border= 
 
Sofia Kolesnikova ; Martin Hub√°lek; Lucie Bedn√°rov√°; Josef Cvańćka; Edward A. Curtis
 
 
Computational Biology
 
 
 
Prediction of genome-wide DNA methylation in repetitive elements border= 
 
Yinan Zheng; Brian T. Joyce ; Lei Liu; Zhou Zhang; Warren A. Kibbe ...
 
 
 
 
MCbiclust: a novel algorithm to discover large-scale functionally related gene sets from massive transcriptomics data collections border= 
 
Robert B. Bentham; Kevin Bryson; Gyorgy Szabadkai
 
 
Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs border= 
 
Tobias Fehlmann; Christina Backes ; Mustafa Kahraman; Jan Haas; Nicole Ludwig ...
 
 
Combinatorial ensemble miRNA target prediction of co-regulation networks with non-prediction data border= 
 
Jason A. Davis; Sita J. Saunders; Martin Mann; Rolf Backofen
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Chd2 regulates chromatin for proper gene expression toward differentiation in mouse embryonic stem cells border= 
 
Yuichiro Semba; Akihito Harada; Kazumitsu Maehara; Shinya Oki; Chikara Meno ...
 
 
Regulatory dynamics of 11p13 suggest a role for EHF in modifying CF lung disease severity border= 
 
Lindsay R. Stolzenburg ; Rui Yang; Jenny L. Kerschner; Sara Fossum; Matthew Xu ...
 
 
 
 
MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation border=  
 
Xianlu L. Peng; Karl K. So; Liangqiang He ; Yu Zhao; Jiajian Zhou ...
 
 
Mediator binds to boundaries of chromosomal interaction domains and to proteins involved in DNA looping, RNA metabolism, chromatin remodeling, and actin assembly border= 
 
RńÉzvan V. Chereji; Vasudha Bharatula; Nils Elfving; Jeanette Blomberg ; Miriam Larsson ...
 
 
Strand-specific CpG hemimethylation, a novel epigenetic modification functional for genomic imprinting border= 
 
Iris Pati√Īo-Parrado; √ lvaro G√≥mez-Jim√©nez; Noelia L√≥pez-S√°nchez; Jos√© M. Frade
 
 
Flipping states: a few key residues decide the winning conformation of the only universally conserved transcription factor border= 
 
Da Shi; Dmitri Svetlov; Ruben Abagyan; Irina Artsimovitch
 
 
Identification of Arabidopsis thaliana upstream open reading frames encoding peptide sequences that cause ribosomal arrest border= 
 
Noriya Hayashi; Shun Sasaki; Hiro Takahashi; Yui Yamashita ; Satoshi Naito ...
 
 
Genome Integrity, Repair and Replication
 
 
 
A phosphorylation-and-ubiquitylation circuitry driving ATR activation and homologous recombination border= 
 
Jean-Christophe Dubois; Ma√Įlyn Yates; Antoine Gaudreau-Lapierre; Genevi√®ve Cl√©ment; Laurent Cappadocia ...
 
 
Bacillus subtilis RecA with DprA'SsbA antagonizes RecX function during natural transformation border= 
 
Shimin Le ; Ester Serrano; Ryo Kawamura; Bego√Īa Carrasco; Jie Yan ...
 
 
FANCJ helicase controls the balance between short- and long-tract gene conversions between sister chromatids border= 
 
Sarmi Nath; Kumar Somyajit ; Anup Mishra; Ralph Scully; Ganesh Nagaraju
 
 
Unencumbered Pol beta lyase activity in nucleosome core particles 
 
Yesenia Rodriguez; Michael J. Howard; Matthew J. Cuneo; Rajendra Prasad ; Samuel H. Wilson
 
 
A novel nucleoid-associated protein coordinates chromosome replication and chromosome partition border= 
 
James A. Taylor; Ga√ęl Panis; Patrick H. Viollier; Gregory T. Marczynski
 
 
Genomics
 
 
 
Distinct regulation of alternative polyadenylation and gene expression by nuclear poly(A) polymerases border= 
 
Weimin Li; Wencheng Li ; Rakesh S. Laishram; Mainul Hoque; Zhe Ji ...
 
 
Integrative and conjugative elements and their hosts: composition, distribution and organization border= 
 
Jean Cury; Marie Touchon; Eduardo P. C. Rocha
 
 
Molecular Biology
 
 
 
The SmAP2 RNA binding motif in the 3≤UTR affects mRNA stability in the crenarchaeum Sulfolobus solfataricus border= 
 
Birgit Märtens; Kundan Sharma; Henning Urlaub; Udo Bläsi
 
 
Genome-wide analysis of influenza viral RNA and nucleoprotein association border= 
 
Nara Lee; Valerie Le Sage; Adalena V. Nanni; Dan J. Snyder ; Vaughn S. Cooper ...
 
 
Coupling transcriptional activation of CRISPR'Cas system and DNA repair genes by Csa3a in Sulfolobus islandicus border= 
 
Tao Liu; Zhenzhen Liu; Qing Ye; Saifu Pan; Xiaodi Wang ...
 
 
The IRES5≤UTR of the dicistrovirus cricket paralysis virus is a type III IRES containing an essential pseudoknot structure border= 
 
Lauriane Gross; Quentin Vicens; Evelyne Einhorn; Audrey Noireterre; Laure Schaeffer ...
 
 
Nucleic Acid Enzymes
 
 
 
The third restriction'modification system from Thermus aquaticus YT-1: solving the riddle of two TaqII specificities border= 
 
Piotr M. Skowron; Brian P. Anton ; Edyta Czajkowska; Joanna Zebrowska; Ewa Sulecka ...
 
 
Mechanistic features of the atypical tRNA m1G9 SPOUT methyltransferase, Trm10 border= 
 
Aiswarya Krishnamohan; Jane E. Jackman
 
 
Structure-based domain assignment in Leishmania infantum EndoG: characterization of a pH-dependent regulatory switch and a C-terminal extension that largely dictates DNA substrate preferences border= 
 
Cristina Oliva ; Pedro A. Sánchez-Murcia; Eva Rico; Ana Bravo; Margarita Menéndez ...
 
 
Engineering human PrimPol into an efficient RNA-dependent-DNA primase/polymerase border= 
 
Rubén Agudo; Patricia A. Calvo ; María I. Martínez-Jiménez; Luis Blanco
 
 
RNA and RNA-protein complexes
 
 
 
Position-dependent effects of regioisomeric methylated adenine and guanine ribonucleosides on translation border= 
 
Changjun You; Xiaoxia Dai; Yinsheng Wang
 
 
Polypyrimidine tract-binding protein (PTB) and PTB-associated splicing factor in CVB3 infection: an ITAF for an ITAF border= 
 
Pratik Dave; Biju George; Divya Khandige Sharma; Saumitra Das
 
 
A mechanism for a single nucleotide intron shift border= 
 
Erzsébet Fekete; Michel Flipphi; Norbert à g; Napsugár Kavalecz ; Gustavo Cerqueira ...
 
 
ALG-5 is a miRNA-associated Argonaute required for proper developmental timing in the Caenorhabditis elegans germline border= 
 
Kristen C. Brown; Joshua M. Svendsen; Rachel M. Tucci; Brooke E. Montgomery; Taiowa A. Montgomery
 
 
The biogenesis pathway of tRNA-derived piRNAs in Bombyx germ cells border= 
 
Shozo Honda ; Takuya Kawamura; Phillipe Loher; Keisuke Morichika; Isidore Rigoutsos ...
 
 
Human ribosomal protein eS1 is engaged in cellular events related to processing and functioning of U11 snRNA border= 
 
Alexander V. Gopanenko; Alexey A. Malygin; Alexey E. Tupikin; Pavel P. Laktionov; Marsel R. Kabilov ...
 
 
Structural Biology
 
 
 
Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu 
 
Andrea F. Moon; John M. Pryor; Dale A. Ramsden; Thomas A. Kunkel ; Katarzyna Bebenek ...
 
 
Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes border= 
 
Gang Sheng; Tasos Gogakos; Jiuyu Wang; Hongtu Zhao; Artem Serganov ...
 
 
CpG and methylation-dependent DNA binding and dynamics of the methylcytosine binding domain 2 protein at the single-molecule level border= 
 
Hai Pan ; Stephanie M. Bilinovich; Parminder Kaur; Robert Riehn; Hong Wang ...
 
 
Synthesis and incorporation of 13 C-labeled DNA building blocks to probe structural dynamics of DNA by NMR border= 
 
Felix Nu√übaumer; Michael Andreas Juen ; Catherina Gasser; Johannes Kremser; Thomas M√ľller ...
 
 
Synthetic Biology and Bioengineering
 
 
 
PhiReX: a programmable and red light-regulated protein expression switch for yeast border= 
 
Lena Hochrein; Fabian Machens ; Katrin Messerschmidt; Bernd Mueller-Roeber
 
 
A systematic comparison of error correction enzymes by next-generation sequencing border= 
 
Nathan B. Lubock; Di Zhang; Angus M. Sidore; George M. Church ; Sriram Kosuri
 
 
Methods Online
 
 
 
EC-tagging allows cell type-specific RNA analysis border= 
 
Naoki Hida; Mohamed Y. Aboukilila; Dana A. Burow; Rakesh Paul; Marc M. Greenberg ...
 
 
Highly efficient preparation of single-stranded DNA rings by T4 ligase at abnormally low Mg(II) concentration border= 
 
Ran An ; Qi Li; Yiqiao Fan; Jing Li; Xiaoming Pan ...
 
 
Understanding mutational effects in digenic diseases border= 
 
Andrea Gazzo; Daniele Raimondi ; Dorien Daneels; Yves Moreau; Guillaume Smits ...
 
 
mRNA detection in budding yeast with single fluorophores border= 
 
Gable M. Wadsworth; Rasesh Y. Parikh; John S. Choy; Harold D. Kim
 
 
A massively parallel strategy for STR marker development, capture, and genotyping 
 
Logan Kistler; Stephen M. Johnson ; Mitchell T. Irwin; Edward E. Louis; Aakrosh Ratan ...
 
 
Information transduction capacity reduces the uncertainties in annotation-free isoform discovery and quantification border= 
 
Yue Deng; Feng Bao; Yang Yang; Xiangyang Ji; Mulong Du ...
 
 
Two-tailed RT-qPCR: a novel method for highly accurate miRNA quantification border= 
 
Peter Androvic; Lukas Valihrach; Julie Elling; Robert Sjoback; Mikael Kubista
 
 
Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments border= 
 
Rene Welch ; Dongjun Chung; Jeffrey Grass; Robert Landick; S√ľnd√ľz KeleŇü
 
 
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