Subject: Nucleic Acids Research Table of Contents for 2 November 2017 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Nucleic Acids Research  
Volume 45 Issue 19
 
2 November 2017
 
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NAR Breakthrough Article
 
 
 
Proteomic identification of histone post-translational modifications and proteins enriched at a DNA double-strand break border= 
 
Pingping Wang; Stephanie Byrum; Faith C. Fowler; Sangita Pal ; Alan J. Tackett ...
 
 
SURVEY AND SUMMARY
 
 
 
The FASTK family of proteins: emerging regulators of mitochondrial RNA biology border= 
 
Alexis A. Jourdain; Johannes Popow; Miguel A. de la Fuente; Jean-Claude Martinou; Paul Anderson ...
 
 
Embraced by eIF3: structural and functional insights into the roles of eIF3 across the translation cycle border= 
 
LeoÅ¡ Shivaya ValáÅ¡ek ; Jakub Zeman; Susan Wagner; Petra Beznosková; Zuzana Pavlíková ...
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Impact of enhanced metabolic stability on pharmacokinetics and pharmacodynamics of GalNAc'siRNA conjugates border= 
 
Jayaprakash K. Nair; Husain Attarwala; Alfica Sehgal; Qianfan Wang; Krishna Aluri ...
 
 
Computational Biology
 
 
 
Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data border= 
 
Cheng Jia; Yu Hu ; Derek Kelly; Junhyong Kim; Mingyao Li ...
 
 
 
 
Separation and assembly of deep sequencing data into discrete sub-population genomes border= 
 
Konstantinos Karagiannis; Vahan Simonyan; Konstantin Chumakov; Raja Mazumder
 
 
ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data border= 
 
David Heller; Ralf Krestel ; Uwe Ohler; Martin Vingron; Annalisa Marsico
 
 
Occurrence and stability of lone pair'Ïeuro stacking interactions between ribose and nucleobases in functional RNAs border= 
 
Mohit Chawla; Edrisse Chermak; Qingyun Zhang ; Janusz M. Bujnicki; Romina Oliva ...
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Functional impacts of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine at a single hemi-modified CpG dinucleotide in a gene promoter border= 
 
Nataliya Kitsera; Julia Allgayer; Edris Parsa; Nadine Geier ; Martin Rossa ...
 
 
Transcription'translation coupling: direct interactions of RNA polymerase with ribosomes and ribosomal subunits border= 
 
Haitian Fan; Adam B. Conn; Preston B. Williams; Stephen Diggs; Joseph Hahm ...
 
 
 
 
p53 controls expression of the DNA deaminase APOBEC3B to limit its potential mutagenic activity in cancer cells border= 
 
Manikandan Periyasamy; Anup K. Singh; Carolina Gemma; Christian Kranjec; Raed Farzan ...
 
 
Developmentally regulated higher-order chromatin interactions orchestrate B cell fate commitment border= 
 
Ravi Boya; Anurupa Devi Yadavalli; Sameena Nikhat; Sreenivasulu Kurukuti; Dasaradhi Palakodeti ...
 
 
Oxidative stress rapidly stabilizes promoter-proximal paused Pol II across the human genome border= 
 
Kyle A. Nilson; Christine K. Lawson; Nicholas J. Mullen; Christopher B. Ball; Benjamin M. Spector ...
 
 
The PRMT5/WDR77 complex regulates alternative splicing through ZNF326 in breast cancer border= 
 
Madhumitha Rengasamy ; Fan Zhang; Ajay Vashisht; Won-Min Song; Francesca Aguilo ...
 
 
DNA residence time is a regulatory factor of transcription repression border= 
 
Karen Clauß; Achim P. Popp ; Lena Schulze; Johannes Hettich; Matthias Reisser ...
 
 
Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli border= 
 
Paramita Sarkar; Amy Switzer; Christine Peters; Joe Pogliano ; Sivaramesh Wigneshweraraj
 
 
Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities border= 
 
Daria Bunina; Martin Å tefl; Florian Huber; Anton Khmelinskii; Matthias Meurer ...
 
 
Enrichment of dynamic chromosomal crosslinks drive phase separation of the nucleolus border= 
 
Caitlin Hult ; David Adalsteinsson; Paula A. Vasquez; Josh Lawrimore; Maggie Bennett ...
 
 
Genome Integrity, Repair and Replication
 
 
 
Kinetics of poly(ADP-ribosyl)ation, but not PARP1 itself, determines the cell fate in response to DNA damage in vitro and in vivo border= 
 
Harald Schuhwerk ; Christopher Bruhn; Kanstantsin Siniuk; Wookee Min; Suheda Erener ...
 
 
Abasic and oxidized ribonucleotides embedded in DNA are processed by human APE1 and not by RNase H2 border= 
 
Matilde Clarissa Malfatti; Sathya Balachander; Giulia Antoniali; Kyung Duk Koh; Christine Saint-Pierre ...
 
 
Short inverted repeats contribute to localized mutability in human somatic cells border= 
 
Xueqing Zou; Sandro Morganella; Dominik Glodzik ; Helen Davies; Yilin Li ...
 
 
Regulation of mitotic recombination between DNA repeats in centromeres border= 
 
Faria Zafar; Akiko K. Okita; Atsushi T. Onaka; Jie Su; Yasuhiro Katahira ...
 
 
Genomics
 
 
 
Insights into interplay between rexinoid signaling and myogenic regulatory factor-associated chromatin state in myogenic differentiation border= 
 
Munerah Hamed; Saadia Khilji; Katherine Dixon; Alexandre Blais; Ilya Ioshikhes ...
 
 
Molecular Biology
 
 
 
RUNX2 expression in thyroid and breast cancer requires the cooperation of three non-redundant enhancers under the control of BRD4 and c-JUN border= 
 
Valentina Sancisi ; Gloria Manzotti; Mila Gugnoni; Teresa Rossi; Greta Gandolfi ...
 
 
A G-quadruplex motif in an envelope gene promoter regulates transcription and virion secretion in HBV genotype B border= 
 
Banhi Biswas; Manish Kandpal; Perumal Vivekanandan
 
 
Role of free DNA ends and protospacer adjacent motifs for CRISPR DNA uptake in Pyrococcus furiosus border= 
 
Masami Shiimori; Sandra C. Garrett; Dwain P. Chambers; Claiborne V. C. Glover, III; Brenton R. Graveley ...
 
 
Nucleic Acid Enzymes
 
 
 
A ˜new lease of life': FnCpf1 possesses DNA cleavage activity for genome editing in human cells border= 
 
Mengjun Tu ; Li Lin; Yilu Cheng; Xiubin He; Huihui Sun ...
 
 
Cmr1 enables efficient RNA and DNA interference of a III-B CRISPR'Cas system by binding to target RNA and crRNA border= 
 
Yingjun Li; Yan Zhang ; Jinzhong Lin; Saifu Pan; Wenyuan Han ...
 
 
Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination border= 
 
Michelle Marasco; Weiyi Li; Michael Lynch ; Craig S. Pikaard
 
 
Insights into RNA polymerase catalysis and adaptive evolution gained from mutational analysis of a locus conferring rifampicin resistance border= 
 
Olga Yurieva; Vadim Nikiforov, Jr; Vadim Nikiforov; Michael O'Donnell; Arkady Mustaev
 
 
RNA and RNA-protein complexes
 
 
 
The RNA chaperone La promotes pre-tRNA maturation via indiscriminate binding of both native and misfolded targets border= 
 
Ana Vakiloroayaei; Neha S. Shah; Marlene Oeffinger; Mark A. Bayfield
 
 
N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3²-end processing border= 
 
Marek Bartosovic; Helena Covelo Molares; Pavlina Gregorova ; Dominika Hrossova; Grzegorz Kudla ...
 
 
Naturally existing isoforms of miR-222 have distinct functions border= 
 
Feng Yu; Katherine A. Pillman; Corine T. Neilsen; John Toubia ; David M. Lawrence ...
 
 
Initiating ribosomes and a 5²/3²-UTR interaction control ribonuclease action to tightly couple B. subtilis hbs mRNA stability with translation border= 
 
Frédérique Braun; Sylvain Durand; Ciarán Condon
 
 
Structural Biology
 
 
 
Involvement of G-triplex and G-hairpin in the multi-pathway folding of human telomeric G-quadruplex border= 
 
Xi-Miao Hou; Yi-Ben Fu ; Wen-Qiang Wu; Lei Wang; Fang-Yuan Teng ...
 
 
A novel TPR'BEN domain interaction mediates PICH'BEND3 association border= 
 
Ganesha P. Pitchai; Manuel Kaulich; Anna H. Bizard; Pablo Mesa ; Qi Yao ...
 
 
Activator Protein-1: redox switch controlling structure and DNA-binding border= 
 
Zhou Yin; Mischa Machius; Eric J. Nestler; Gabby Rudenko
 
 
Altering the speed of a DNA packaging motor from bacteriophage T4 border= 
 
Siying Lin; Tanfis I. Alam ; Vishal I. Kottadiel; Carl J. VanGessel; Wei-Chun Tang ...
 
 
Synthetic Biology and Bioengineering
 
 
 
In vitro transcription'translation using bacterial genome as a template to reconstitute intracellular profile border= 
 
Kei Fujiwara; Tsunehito Sawamura ; Tatsuya Niwa; Tatsuki Deyama; Shin-ichiro M. Nomura ...
 
 
Addressable configurations of DNA nanostructures for rewritable memory border= 
 
Arun Richard Chandrasekaran; Oksana Levchenko; Dhruv S. Patel; Molly MacIsaac; Ken Halvorsen
 
 
Methods Online
 
 
 
Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy border= 
 
John M. Bell; Billy T. Lau; Stephanie U. Greer; Christina Wood-Bouwens; Li C. Xia ...
 
 
HiTAD: detecting the structural and functional hierarchies of topologically associating domains from chromatin interactions border= 
 
Xiao-Tao Wang ; Wang Cui; Cheng Peng
 
 
Programming sites of meiotic crossovers using Spo11 fusion proteins border= 
 
Roberta Sarno; Yoan Vicq; Norio Uematsu; Marine Luka; Clement Lapierre ...
 
 
CRISPR-mediated isolation of specific megabase segments of genomic DNA border= 
 
Pamela E. Bennett-Baker ; Jacob L. Mueller
 
 
Network embedding-based representation learning for single cell RNA-seq data border= 
 
Xiangyu Li; Weizheng Chen; Yang Chen; Xuegong Zhang; Jin Gu ...
 
 
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