Subject: Nucleic Acids Research Table of Contents for 6 July 2018 ------=_Part_1149063890.1531158956157 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1149063890.1531158956157 Content-Type: text/html;charset=UTF-8 Oxford Academic
                                 

 
 
 
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Nucleic Acids Research  
Volume 46 Issue 12
 
6 July 2018
 
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An integrative model for alternative polyadenylation, IntMAP, delineates mTOR-modulated endoplasmic reticulum stress response border= 
 
Jae-Woong Chang; Wei Zhang; Hsin-Sung Yeh; Meeyeon Park ; Chengguo Yao ...
 
 
 
 
 
Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis border= 
 
Lovorka Stojic; Aaron T L Lun ; Jasmin Mangei; Patrice Mascalchi; Valentina Quarantotti ...
 
 
NAR Breakthrough Article
 
 
 
Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction border= 
 
Jithesh Kottur; Deepak T Nair
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Redox-dependent control of i-Motif DNA structure using copper cations border= 
 
Mahmoud AS Abdelhamid; László Fábián; Colin J MacDonald; Myles R Cheesman; Andrew J Gates ...
 
 
G-quadruplex binding ability of TLS/FUS depends on the beta -spiral structure of the RGG domain border= 
 
Ryota Yagi ; Takatsugu Miyazaki; Takanori Oyoshi
 
 
Nucleoside analogs to manage sequence divergence in nucleic acid amplification and SNP detection border= 
 
Zunyi Yang; Hyo-Joong Kim; Jennifer T Le; Chris McLendon ; Kevin M Bradley ...
 
 
N4-acyl-2²-deoxycytidine-5²-triphosphates for the enzymatic synthesis of modified DNA border= 
 
Jevgenija Jakubovska; Daiva TauraitÄ-; Lukas BirÅ¡tonas; Rolandas MeÅ¡kys
 
 
Computational Biology
 
 
 
Properties of gene expression and chromatin structure with mechanically regulated elongation border=  
 
Stuart A Sevier; Herbert Levine
 
 
Diffusion of ring-shaped proteins along DNA: case study of sliding clamps border= 
 
Dina Daitchman; Harry M Greenblatt ; Yaakov Levy
 
 
Discovery of two-level modular organization from matched genomic data via joint matrix tri-factorization border= 
 
Jinyu Chen; Shihua Zhang
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Global DNA methylation synergistically regulates the nuclear and mitochondrial genomes in glioblastoma cells border= 
 
Xin Sun; Jacqueline Johnson; Justin C St. John
 
 
Antisense transcriptional interference mediates condition-specific gene repression in budding yeast border= 
 
Alicia Nevers; Antonia Doyen; Christophe Malabat ; Bertrand Néron; Thomas Kergrohen ...
 
 
Sin3a'Tet1 interaction activates gene transcription and is required for embryonic stem cell pluripotency border= 
 
Fugui Zhu; Qianshu Zhu; Dan Ye; Qingquan Zhang ; Yiwei Yang ...
 
 
Dynamic chromosomal tuning of a novel GAU1 lncing driver at chr12p13.32 accelerates tumorigenesis border= 
 
Peiwei Chai; Ruobing Jia; Renbing Jia; Hui Pan; Shaoyun Wang ...
 
 
Cooperative binding of ApiAP2 transcription factors is crucial for the expression of virulence genes in Toxoplasma gondii border= 
 
Kevin M Lesage; Ludovic Huot; Thomas Mouveaux; Flavie Courjol; Jean-Michel Saliou ...
 
 
Alternative splicing analysis in human monocytes and macrophages reveals MBNL1 as major regulator border= 
 
Hongfei Liu; Paolo A Lorenzini ; Fan Zhang; Shaohai Xu; Mei Su M Wong ...
 
 
Genome Integrity, Repair and Replication
 
 
 
CHD3 and CHD4 recruitment and chromatin remodeling activity at DNA breaks is promoted by early poly(ADP-ribose)-dependent chromatin relaxation border= 
 
Rebecca Smith; Hafida Sellou; Catherine Chapuis; Sébastien Huet ; Gyula Timinszky
 
 
ComM is a hexameric helicase that promotes branch migration during natural transformation in diverse Gram-negative species border= 
 
Thomas M Nero; Triana N Dalia; Joseph Che-Yen Wang; David T Kysela; Matthew L Bochman ...
 
 
Peripheral re-localization of constitutive heterochromatin advances its replication timing and impairs maintenance of silencing marks border= 
 
Kathrin S Heinz; Corella S Casas-Delucchi; Timea Török; Dusan Cmarko; Alexander Rapp ...
 
 
MPK-1/ERK pathway regulates DNA damage response during development through DAF-16/FOXO border= 
 
Julien N Bianco; Björn Schumacher
 
 
Origin recognition is the predominant role for DnaA-ATP in initiation of chromosome replication border= 
 
Julia E Grimwade ; Tania A Rozgaja; Rajat Gupta; Kyle Dyson; Prassanna Rao ...
 
 
Bacterial EndoMS/NucS acts as a clamp-mediated mismatch endonuclease to prevent asymmetric accumulation of replication errors border= 
 
Norihiko Takemoto ; Itaru Numata; Masayuki Su'etsugu; Tohru Miyoshi-Akiyama
 
 
Genomics
 
 
 
PUF60-activated exons uncover altered 3² splice-site selection by germline missense mutations in a single RRM border= 
 
Jana Královičová; Ivana Å evčíková; Eva Stejskalová; Mina Obuća ; Michael Hiller ...
 
 
Molecular Biology
 
 
 
Identification of a novel TIF-IA'NF-kappa B nucleolar stress response pathway border= 
 
Jingyu Chen ; Ian T Lobb; Pierre Morin; Sonia M Novo; James Simpson ...
 
 
Activation of the mismatch-specific endonuclease EndoMS/NucS by the replication clamp is required for high fidelity DNA replication border= 
 
Sonoko Ishino ; Stéphane Skouloubris; Hanae Kudo; Caroline l'Hermitte-Stead; Asmae Es-Sadik ...
 
 
The translational landscape of Arabidopsis mitochondria border= 
 
Noelya Planchard; Pierre Bertin ; Martine Quadrado; Céline Dargel-Graffin; Isabelle Hatin ...
 
 
Nucleic Acid Enzymes
 
 
 
Single-site DNA cleavage by Type III restriction endonuclease requires a site-bound enzyme and a trans-acting enzyme that are ATPase-activated border= 
 
Ishtiyaq Ahmad; Manasi Kulkarni; Aathira Gopinath; Kayarat Saikrishnan
 
 
A minimal threshold of FANCJ helicase activity is required for its response to replication stress or double-strand break repair 
 
Sanjay Kumar Bharti ; Joshua A Sommers; Sanket Awate; Marina A Bellani; Irfan Khan ...
 
 
The structure of human Nocturnin reveals a conserved ribonuclease domain that represses target transcript translation and abundance in cells border= 
 
Elizabeth T. Abshire ; Jennifer Chasseur; Jennifer A Bohn; Paul A Del Rizzo; Peter L Freddolino ...
 
 
Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries border= 
 
Irina Randrianjatovo-Gbalou ; Sandrine Rosario; Odile Sismeiro; Hugo Varet; Rachel Legendre ...
 
 
RNA and RNA-protein complexes
 
 
 
IGF2BP1 enhances an aggressive tumor cell phenotype by impairing miRNA-directed downregulation of oncogenic factors border=  
 
Simon Müller; Nadine Bley; Markus Glaß ; Bianca Busch; Vanessa Rousseau ...
 
 
DDX49 is an RNA helicase that affects translation by regulating mRNA export and the levels of pre-ribosomal RNA border= 
 
Sharad Awasthi; Mamta Verma; Arun Mahesh; Mohd Imran K. Khan ; Gayathri Govindaraju ...
 
 
Control of mRNA decapping by autoinhibition border= 
 
David R Paquette; Ryan W Tibble; Tristan S Daifuku; John D Gross
 
 
Eukaryotic translation initiation factor 4AII contributes to microRNA-122 regulation of hepatitis C virus replication border= 
 
Choudhary Shoaib Ahmed ; Poppy L Winlow; Aimee L Parsons; Catherine L Jopling
 
 
HITS-CLIP in various brain areas reveals new targets and new modalities of RNA binding by fragile X mental retardation protein border=  
 
Thomas Maurin; Kevin Lebrigand; Sara Castagnola ; Agnès Paquet; Marielle Jarjat ...
 
 
Structural Biology
 
 
 
DNA base sequence effects on bulky lesion-induced conformational heterogeneity during DNA replication 
 
Ang Cai ; Katie A Wilson; Satyakam Patnaik; Stacey D Wetmore; Bongsup P Cho
 
 
Functional insights into the Streptococcus pneumoniae HicBA toxin'antitoxin system based on a structural study border= 
 
Do-Hee Kim; Sung-Min Kang ; Sung Jean Park; Chenglong Jin; Hye-Jin Yoon ...
 
 
Synthetic Biology and Bioengineering
 
 
 
Oligonucleotide-mediated tRNA sequestration enables one-pot sense codon reassignment in vitro border= 
 
Zhenling Cui; Yue Wu; Sergey Mureev; Kirill Alexandrov
 
 
Methods Online
 
 
 
Direct transfection of clonal organoids in Matrigel microbeads: a promising approach toward organoid-based genetic screens border= 
 
Bastien Laperrousaz ; Stephanie Porte; Sophie Gerbaud; Ville Härmä; Frédérique Kermarrec ...
 
 
Paired D10A Cas9 nickases are sometimes more efficient than individual nucleases for gene disruption border= 
 
Ramu Gopalappa; Bharathi Suresh; Suresh Ramakrishna; Hyongbum (Henry) Kim
 
 
A novel method for improved accuracy of transcription factor binding site prediction border= 
 
Abdullah M Khamis; Olaa Motwalli; Romina Oliva; Boris R Jankovic ; Yulia A Medvedeva ...
 
 
dUTPs conjugated with zwitterionic Cy3 or Cy5 fluorophore analogues are effective substrates for DNA amplification and labelling by Taq polymerase border= 
 
Olga A Zasedateleva; Vadim A Vasiliskov; Sergey A Surzhikov; Viktoriya E Kuznetsova; Valeriy E Shershov ...
 
 
Enhanced detection of microsatellite instability using pre-PCR elimination of wild-type DNA homo-polymers in tissue and liquid biopsies border= 
 
Ioannis Ladas; Fangyan Yu; Ka Wai Leong; Mariana Fitarelli-Kiehl; Chen Song ...
 
 
Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq border= 
 
Michael J Guertin; Amy E Cullen ; Florian Markowetz; Andrew N Holding
 
 
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