Subject: Nucleic Acids Research Table of Contents for 19 September 2017 Oxford Academic
 
 
 
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New issue alert
 
Nucleic Acids Research  
Volume 45 Issue 16
 
19 September 2017
 
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Chemical Biology and Nucleic Acid Chemistry
 
 
 
A synthetic DNA-binding inhibitor of SOX2 guides human induced pluripotent stem cells to differentiate into mesoderm border= 
 
Junichi Taniguchi; Ganesh N. Pandian; Takuya Hidaka; Kaori Hashiya ; Toshikazu Bando ...
 
 
Computational Biology
 
 
 
Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning 
 
Alexey K. Shaytan; Hua Xiao; Grigoriy A. Armeev; Carl Wu; David Landsman ...
 
 
Automatic identification of informative regions with epigenomic changes associated to hematopoiesis border= 
 
Enrique Carrillo-de-Santa-Pau; David Juan; Vera Pancaldi; Felipe Were; Ignacio Martin-Subero ...
 
 
CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome border= 
 
Zijun Zhang; Yi Xing
 
 
Data Resources and Analyses
 
 
 
Accumulation of histone variant H3.3 with age is associated with profound changes in the histone methylation landscape border= 
 
Andrey Tvardovskiy; Veit Schw├Ąmmle; Stefan J. Kempf; Adelina Rogowska-Wrzesinska; Ole N. Jensen
 
 
 
 
A comprehensive, cell specific microRNA catalogue of human peripheral blood border= 
 
Simonas Juzenas; Geetha Venkatesh; Matthias H├╝benthal; Marc P. Hoeppner ; Zhipei Gracie Du ...
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
The ribosome assembly gene network is controlled by the feedback regulation of transcription elongation border= 
 
Fernando G├│mez-Herreros; Thanasis Margaritis; Olga Rodr├şguez-Gal├ín; Vicent Pelechano ; Victoria Begley ...
 
 
Identification of multiple roles for histone acetyltransferase 1 in replication-coupled chromatin assembly border= 
 
Paula A. Agudelo Garcia; Michael E. Hoover; Pei Zhang; Prabakaran Nagarajan; Michael A. Freitas ...
 
 
XIAP upregulates expression of HIF target genes by targeting HIF1alpha for Lys63-linked polyubiquitination border= 
 
Catherine V. Park ; Iglika G. Ivanova; Niall S. Kenneth
 
 
Crosstalk between histone modifications indicates that inhibition of arginine methyltransferase CARM1 activity reverses HIV latency border= 
 
Zheng Zhang; Bryan C. Nikolai; Leah A. Gates; Sung Yun Jung ; Edward B. Siwak ...
 
 
 
 
Recruitment and delivery of the fission yeast Rst2 transcription factor via a local genome structure counteracts repression by Tup1-family corepressors border= 
 
Ryuta Asada; Miki Umeda; Akira Adachi; Satoshi Senmatsu; Takuya Abe ...
 
 
Regulation of chromatin folding by conformational variations of nucleosome linker DNA border= 
 
Jenna M. Buckwalter ; Davood Norouzi; Anna Harutyunyan; Victor B. Zhurkin; Sergei A. Grigoryev
 
 
Cohesin acetyltransferase Esco2 regulates SAC and kinetochore functions via maintaining H4K16 acetylation during mouse oocyte meiosis border= 
 
Yajuan Lu ; Xiaoxin Dai; Mianqun Zhang; Yilong Miao; Changyin Zhou ...
 
 
A novel requirement for DROSHA in maintenance of mammalian CG methylation border= 
 
Athanasia Stathopoulou; Jyoti B. Chhetri ; John C. Ambrose; Pierre-Olivier Est├Ęve; Lexiang Ji ...
 
 
Genome Integrity, Repair and Replication
 
 
 
Monitoring Replication Protein A (RPA) dynamics in homologous recombination through site-specific incorporation of non-canonical amino acids border= 
 
Nilisha Pokhrel ; Sofia Origanti; Eric Parker Davenport; Disha Gandhi; Kyle Kaniecki ...
 
 
Human DNA polymerase delta double-mutant D316A;E318A interferes with DNA mismatch repair in vitro  border= 
 
Dekang Liu; Jane H. Frederiksen ; Sascha E. Liberti; Anne L├╝tzen; Guido Keijzers ...
 
 
Phosphorylation regulates human poleta stability and damage bypass throughout the cell cycle border= 
 
Federica Bertoletti; Valentina Cea; Chih-Chao Liang; Taiba Lanati ; Antonio Maffia ...
 
 
STN1'POLA2 interaction provides a basis for primase-pol alpha stimulation by human STN1 border= 
 
Swapna Ganduri; Neal F. Lue
 
 
Systematic analysis of DNA crosslink repair pathways during development and aging in Caenorhabditis elegans 
 
David M. Wilson, III; Matthias Rieckher; Ashley B. Williams; Bj├Ârn Schumacher
 
 
Genomics
 
 
 
A germline-limited piggyBac transposase gene is required for precise excision in Tetrahymena genome rearrangement border= 
 
Lifang Feng; Guangying Wang ; Eileen P. Hamilton; Jie Xiong; Guanxiong Yan ...
 
 
Widespread intra-dependencies in the removal of introns from human transcripts border= 
 
Seong Won Kim; Allison J. Taggart; Claire Heintzelman; Kamil J. Cygan ; Caitlin G. Hull ...
 
 
Molecular Biology
 
 
 
Regulation of HuR structure and function by dihydrotanshinone-I border= 
 
Preet Lal; Linda Cerofolini; Vito Giuseppe D'Agostino; Chiara Zucal; Carmelo Fuccio ...
 
 
Antisense oligonucleotides targeting translation inhibitory elements in 5▓ UTRs can selectively increase protein levels border= 
 
Xue-hai Liang ; Hong Sun; Wen Shen; Shiyu Wang; Joyee Yao ...
 
 
Number of inadvertent RNA targets for morpholino knockdown in Danio rerio is largely underestimated: evidence from the study of Ser/Arg-rich splicing factors border= 
 
Marine Joris; Marie Schloesser ; Denis Baurain; Marc Hanikenne; Marc Muller ...
 
 
Concerted action of two 3▓ cap-independent translation enhancers increases the competitive strength of translated viral genomes border= 
 
Zhiyou Du; Olga M. Alekhina; Konstantin S. Vassilenko ; Anne E. Simon
 
 
Co-produced natural ketolides methymycin and pikromycin inhibit bacterial growth by preventing synthesis of a limited number of proteins border= 
 
Mashal M. Almutairi; Maxim S. Svetlov; Douglas A. Hansen; Nelli F. Khabibullina; Dorota Klepacki ...
 
 
Nucleic Acid Enzymes
 
 
 
UbaLAI is a monomeric Type IIE restriction enzyme border= 
 
Giedrius Sasnauskas ; Giedr─- Tamulaitien─-; Gintautas Tamulaitis; Jelena ─'aly┼íeva; Migl─- Laime ...
 
 
Derivatives of Bst -like Gss-polymerase with improved processivity and inhibitor tolerance border= 
 
Igor P. Oscorbin; Ekaterina A. Belousova ; Ulyana A. Boyarskikh; Aleksandr I. Zakabunin; Evgeny A. Khrapov ...
 
 
Activities of gyrase and topoisomerase IV on positively supercoiled DNA border= 
 
Rachel E. Ashley; Andrew Dittmore; Sylvia A. McPherson; Charles L. Turnbough, Jr; Keir C. Neuman ...
 
 
RNA and RNA-protein complexes
 
 
 
The important conformational plasticity of DsrA sRNA for adapting multiple target regulation border= 
 
Pengzhi Wu; Xiaodan Liu; Lingna Yang; Yitong Sun ; Qingguo Gong ...
 
 
ALYREF mainly binds to the 5▓ and the 3▓ regions of the mRNA in vivo border= 
 
Min Shi; Heng Zhang; Xudong Wu; Zhisong He; Lantian Wang ...
 
 
hnRNP L controls HPV16 RNA polyadenylation and splicing in an Akt kinase-dependent manner border= 
 
Naoko Kajitani ; Jacob Glahder; Chengjun Wu; Haoran Yu; Kersti Nilsson ...
 
 
The conserved AU dinucleotide at the 5▓ end of nascent U1 snRNA is optimized for the interaction with nuclear cap-binding-complex border= 
 
Chung-Shu Yeh ; Shang-Lin Chang; Jui ş-Hui Chen; Hsuan-Kai Wang; Yue-Chang Chou ...
 
 
A structural map of oncomiR-1 at single-nucleotide resolution border= 
 
Saikat Chakraborty; Yamuna Krishnan
 
 
Tuning RNA folding and function through rational design of junction topology border= 
 
May Daher ; Anthony M. Mustoe; Alex Morriss-Andrews; Charles L. Brooks III; Nils G. Walter
 
 
In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding border= 
 
Danny Incarnato; Edoardo Morandi ; Francesca Anselmi; Lisa M. Simon; Giulia Basile ...
 
 
Structural Biology
 
 
 
Crystal structure of an engineered, HIV-specific recombinase for removal of integrated proviral DNA border= 
 
Gretchen Meinke; Janet Karpinski ; Frank Buchholz; Andrew Bohm
 
 
A novel non-canonical PIP-box mediates PARG interaction with PCNA border= 
 
Tanja Kaufmann; Irina Grishkovskaya; Anton A. Polyansky; Sebastian Kostrhon; Eva Kukolj ...
 
 
The fused SnoaL_2 domain in the Mycobacterium tuberculosis sigma factor ¤âJ modulates promoter recognition border= 
 
Kapil Goutam ; Arvind K. Gupta; Balasubramanian Gopal
 
 
Mechanistic insight into how multidrug resistant Acinetobacter baumannii response regulator AdeR recognizes an intercistronic region border= 
 
Yurong Wen; Zhenlin Ouyang; Yue Yu; Xiaorong Zhou ; Yingmei Pei ...
 
 
Synthetic Biology and Bioengineering
 
 
 
Blocking the RecA activity and SOS-response in bacteria with a short alpha -helical peptide border= 
 
Alexander Yakimov; Georgii Pobegalov; Irina Bakhlanova; Mikhail Khodorkovskii; Michael Petukhov ...
 
 
Model-based design of RNA hybridization networks implemented in living cells border= 
 
Guillermo Rodrigo ; Satya Prakash; Shensi Shen; Eszter Majer; Jos├ę-Antonio Dar├▓s ...
 
 
Corrigendum
 
 
 
CAF-1-induced oligomerization of histones H3/H4 and mutually exclusive interactions with Asf1 guide H3/H4 transitions among histone chaperones and DNA border= 
 
Wallace H. Liu ; Sarah C. Roemer; Alex M. Port; Mair E.A. Churchill
 
 
A novel requirement for DROSHA in maintenance of mammalian CG methylation border= 
 
Athanasia Stathopoulou; Jyoti B. Chhetri; John C. Ambrose; Pierre-Olivier Est├Ęve; Lexiang Ji ...
 
 
Retraction
 
 
 
Yeast CAF-1 assembles histone (H3-H4) 2 tetramers prior to DNA deposition border= 
 
Duane D. Winkler; Hui Zhou; Mohd A. Dar; Zhiguo Zhang; Karolin Luger
 
 
Methods Online
 
 
 
Combining asymmetric 13C-labeling and isotopic filter/edit NOESY: a novel strategy for rapid and logical RNA resonance assignment border= 
 
Regan M. LeBlanc; Andrew P. Longhini; Stuart F.J. Le Grice; Bruce A. Johnson; Theodore K. Dayie
 
 
Controlled re-activation of epigenetically silenced Tet promoter-driven transgene expression by targeted demethylation border= 
 
Natascha G├Âdecke; Lisha Zha; Shawal Spencer; Sara Behme; Pamela Riemer ...
 
 
Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state border= 
 
Shaked Afik; Kathleen B. Yates; Kevin Bi ; Samuel Darko; Jernej Godec ...
 
 
Detecting gene subnetworks under selection in biological pathways border= 
 
Alexandre Gouy; Jos├ęphine T. Daub; Laurent Excoffier
 
 
SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments border= 
 
Pawe┼é Pi─.tkowski ; Jagoda Jab┼éo┼"ska; Adriana ┼╗y┼éa; Dorota Niedzia┼éek; Dorota Matelska ...
 
 
De novo pathway-based biomarker identification border= 
 
Nicolas Alcaraz; Markus List ; Richa Batra; Fabio Vandin; Henrik J. Ditzel ...
 
 
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