Subject: Nucleic Acids Research Table of Contents for 19 September 2019 ------=_Part_1710023663.1569005318355 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1710023663.1569005318355 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Nucleic Acids Research  
Volume 47 Issue 16
 
19 September 2019
 
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NAR Breakthrough Article
 
 
 
Single-molecule visualization reveals the damage search mechanism for the human NER protein XPC-RAD23B border= 
 
Na Young Cheon ; Hyun-Suk Kim; Jung-Eun Yeo; Orlando D Schärer; Ja Yil Lee
 
 
 
Survey and Summary
 
 
 
DNA polymerase zeta in DNA replication and repair border= 
 
Sara K Martin; Richard D Wood
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Molecular affinity rulers: systematic evaluation of DNA aptamers for their applicabilities in ELISA border= 
 
Michiko Kimoto ; Yun Wei Shermane Lim; Ichiro Hirao
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine border= 
 
Jie Yang ; John R Horton; Jia Li; Yun Huang; Xing Zhang ...
 
 
Structural basis of specific DNA binding by the transcription factor ZBTB24 border= 
 
Ren Ren ; Swanand Hardikar; John R Horton; Yue Lu; Yang Zeng ...
 
 
A novel histone H4 variant H4G regulates rDNA transcription in breast cancer border= 
 
Mengping Long ; Xulun Sun; Wenjin Shi; An Yanru; Sophia T C Leung ...
 
 
The nucleosome acidic patch directly interacts with subunits of the Paf1 and FACT complexes and controls chromatin architecture in vivo  border= 
 
Christine E Cucinotta; A Elizabeth Hildreth ; Brendan M McShane; Margaret K Shirra; Karen M Arndt
 
 
Enhancer-mediated enrichment of interacting JMJD3'DDX21 to ENPP2 locus prevents R-loop formation and promotes transcription border= 
 
Deborah Argaud; Marie-Chloé Boulanger; Arnaud Chignon; Ghada Mkannez; Patrick Mathieu
 
 
Gcn5-mediated acetylation at MBF-regulated promoters induces the G1/S transcriptional wave border= 
 
Alberto González-Medina ; Elena Hidalgo; José Ayté
 
 
Inositol pyrophosphates impact phosphate homeostasis via modulation of RNA 3² processing and transcription termination border= 
 
Ana M Sanchez ; Angad Garg; Stewart Shuman; Beate Schwer
 
 
Super-resolution microscopy reveals how histone tail acetylation affects DNA compaction within nucleosomes in vivo  border= 
 
Jason Otterstrom; Alvaro Castells-Garcia ; Chiara Vicario; Pablo A Gomez-Garcia; Maria Pia Cosma ...
 
 
Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes border= 
 
Weiyu Zhang ; Fuquan Chen; Ruiqing Chen; Dan Xie; Jiao Yang ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
MORC2 regulates DNA damage response through a PARP1-dependent pathway border= 
 
Lin Zhang ; Da-Qiang Li
 
 
Symmetric activity of DNA polymerases at and recruitment of exonuclease ExoR and of PolA to the Bacillus subtilis replication forks border= 
 
Rogelio Hernández-Tamayo; Luis M Oviedo-Bocanegra; Georg Fritz; Peter L Graumann
 
 
Nucleotide excision repair of abasic DNA lesions border=  
 
Nataliya Kitsera; Marta Rodriguez-Alvarez; Steffen Emmert; Thomas Carell; Andriy Khobta
 
 
Cockayne syndrome group B deficiency reduces H3K9me3 chromatin remodeler SETDB1 and exacerbates cellular aging 
 
Jong-Hyuk Lee; Tyler G Demarest; Mansi Babbar ; Edward W Kim; Mustafa N Okur ...
 
 
A PARP1'BRG1'SIRT1 axis promotes HR repair by reducing nucleosome density at DNA damage sites border= 
 
Yu Chen ; Haiping Zhang; Zhu Xu; Huanyin Tang; Anke Geng ...
 
 
Are the intrinsically disordered linkers involved in SSB binding to accessory proteins? border= 
 
Min Kyung Shinn ; Alexander G Kozlov; Binh Nguyen; Wlodek M Bujalowski; Timothy M Lohman
 
 
Complementary roles of Pif1 helicase and single stranded DNA binding proteins in stimulating DNA replication through G-quadruplexes border= 
 
Melanie A Sparks ; Saurabh P Singh; Peter M Burgers; Roberto Galletto
 
 
 
Molecular Biology
 
 
 
Extensive transcriptional responses are co-ordinated by microRNAs as revealed by Exon'Intron Split Analysis (EISA) border= 
 
Katherine A Pillman ; Kaitlin G Scheer; Emily Hackett-Jones; Klay Saunders; Andrew G Bert ...
 
 
The general mRNA exporters Mex67 and Mtr2 play distinct roles in nuclear export of tRNAs in Trypanosoma brucei  border= 
 
Eva Hegedűsová; Sneha Kulkarni ; Brandon Burgman; Juan D Alfonzo; ZdenÄ›k Paris
 
 
CRISPR DNA elements controlling site-specific spacer integration and proper repeat length by a Type II CRISPR'Cas system border= 
 
Jenny G Kim ; Sandra Garrett; Yunzhou Wei; Brenton R Graveley; Michael P Terns
 
 
Citrus exocortis viroid causes ribosomal stress in tomato plants border= 
 
Patrick Cottilli ; Borja Belda-Palazón; Charith Raj Adkar-Purushothama; Jean-Pierre Perreault; Enrico Schleiff ...
 
 
 
Nucleic Acid Enzymes
 
 
 
Newly acquired N-terminal extension targets threonyl-tRNA synthetase-like protein into the multiple tRNA synthetase complex border= 
 
Xiao-Long Zhou ; Yun Chen; Qi-Yu Zeng; Zhi-Rong Ruan; Pengfei Fang ...
 
 
Mechanism of allosteric activation of human mRNA cap methyltransferase (RNMT) by RAM: insights from accelerated molecular dynamics simulations border= 
 
Juan A Bueren-Calabuig ; Marcus G. Bage; Victoria H Cowling; Andrei V Pisliakov
 
 
Zika virus NS3 is a canonical RNA helicase stimulated by NS5 RNA polymerase border= 
 
Shan Xu ; Yali Ci; Leijie Wang; Yang Yang; Leiliang Zhang ...
 
 
Completion of LINE integration involves an open ˜4-way' branched DNA intermediate border= 
 
Brijesh B Khadgi ; Aruna Govindaraju; Shawn M Christensen
 
 
 
RNA and RNA-protein complexes
 
 
 
NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs border= 
 
Lindsey Van Haute ; Song-Yi Lee; Beverly J McCann; Christopher A Powell; Dhiru Bansal ...
 
 
Mammalian NSUN2 introduces 5-methylcytidines into mitochondrial tRNAs border= 
 
Saori Shinoda ; Sho Kitagawa; Shinichi Nakagawa; Fan-Yan Wei; Kazuhito Tomizawa ...
 
 
Biogenesis of RNase P RNA from an intron requires co-assembly with cognate protein subunits border= 
 
Geeta Palsule ; Venkat Gopalan; Amanda Simcox
 
 
An improved method for circular RNA purification using RNase R that efficiently removes linear RNAs containing G-quadruplexes or structured 3² ends border= 
 
Mei-Sheng Xiao ; Jeremy E Wilusz
 
 
Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity 
 
Chen Qiu; Robert C Dutcher; Douglas F Porter ; Yoav Arava; Marvin Wickens ...
 
 
Functional interplay between DEAD-box RNA helicases Ded1 and Dbp1 in preinitiation complex attachment and scanning on structured mRNAs in vivo 
 
Neelam Dabas Sen; Neha Gupta; Stuart K. Archer ; Thomas Preiss; Jon R Lorsch ...
 
 
A role for the Saccharomyces cerevisiae ABCF protein New1 in translation termination/recycling border= 
 
Villu Kasari; Agnieszka A Pochopien; Tõnu Margus; Victoriia Murina; Kathryn Turnbull ...
 
 
Polynucleotide phosphorylase promotes the stability and function of Hfq-binding sRNAs by degrading target mRNA-derived fragments border= 
 
Todd A Cameron ; Lisa M Matz; Dhriti Sinha; Nicholas R De Lay
 
 
Translation-dependent unwinding of stem'loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs border= 
 
Takashi Mino ; Noriki Iwai; Masayuki Endo; Kentaro Inoue; Kotaro Akaki ...
 
 
 
Structural Biology
 
 
 
Specificity of protein'DNA interactions in hypersaline environment: structural studies on complexes of Halobacterium salinarum oxidative stress-dependent protein hsRosR border= 
 
Nitzan Kutnowski; Fania Shmulevich ; Geula Davidov; Anat Shahar; Dudy Bar-Zvi ...
 
 
Cooperative DNA binding by proteins through DNA shape complementarity border= 
 
Stephen P Hancock ; Duilio Cascio; Reid C Johnson
 
 
Sharp kinking of a coiled-coil in MutS allows DNA binding and release border= 
 
Doreth Bhairosing-Kok ; Flora S Groothuizen; Alexander Fish; Shreya Dharadhar; Herrie H K Winterwerp ...
 
 
Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation border= 
 
Roshan Satange ; Chien-Ying Chuang; Stephen Neidle; Ming-Hon Hou
 
 
 
Synthetic Biology and Bioengineering
 
 
 
Engineering DNA recognition and allosteric response properties of TetR family proteins by using a module-swapping strategy border= 
 
Rey P Dimas ; Benjamin R Jordan; Xian-Li Jiang; Catherine Martini; Joseph S Glavy ...
 
 
 
Methods Online
 
 
 
HMMRATAC: a Hidden Markov ModeleR for ATAC-seq border= 
 
Evan D Tarbell; Tao Liu
 
 
Deconvolution of nucleic-acid length distributions: a gel electrophoresis analysis tool and applications border= 
 
Riccardo Ziraldo ; Massa J Shoura; Andrew Z Fire; Stephen D Levene
 
 
SMARTer single cell total RNA sequencing border=  
 
Karen Verboom; Celine Everaert; Nathalie Bolduc ; Kenneth J Livak; Nurten Yigit ...
 
 
Evolutionary coupling analysis identifies the impact of disease-associated variants at less-conserved sites border= 
 
Donghyo Kim ; Seong Kyu Han; Kwanghwan Lee; Inhae Kim; JungHo Kong ...
 
 
CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing border= 
 
Jurrian K de Kanter ; Philip Lijnzaad; Tito Candelli; Thanasis Margaritis; Frank C P Holstege
 
 
WITER: a powerful method for estimation of cancer-driver genes using a weighted iterative regression modelling background mutation counts border= 
 
Lin Jiang ; Jingjing Zheng; Johnny S H Kwan; Sheng Dai; Cong Li ...
 
 
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