Subject: Nucleic Acids Research Table of Contents for 18 November 2019 ------=_Part_50119054.1573778892286 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** {Nucleic Acids Research} *** Volume 47, Issue 20, 18 November 2019 Read this issue (https://academic.oup.com/nar/issue/47/20) ------------------------------ NAR Cancer is now accepting submissions! New Open Access journal NAR Cancer publishes original research, Survey and Summary articles at the intersection of the nucleic acids research and cancer fields, including cancer computational biology and data resources, DNA damage sensing and repair, gene regulation and chromatin, genomics, methods, nucleic acid-based therapeutics, and structural biology. Submit your research. ------------------------------ DNA nanotechnology approaches for microRNA detection and diagnosis Arun Richard Chandrasekaran, Jibin Abraham Punnoose, Lifeng Zhou, Paromita Dey, Bijan K Dey (https://academic.oup.com/nar/article/47/20/10489/5530312) iDamage: a method to integrate modified DNA into the yeast genome Katarzyna H Masłowska, Luisa Laureti, Vincent Pagès (https://academic.oup.com/nar/article/47/20/e124/5550325) Ularcirc: visualization and enhanced analysis of circular RNAs via back and canonical forward splicing David T Humphreys, Nicolas Fossat, Madeleine Demuth, Patrick P L Tam, Joshua W K Ho (https://academic.oup.com/nar/article/47/20/e123/5552786) Detection of internal N7-methylguanosine (m7G) RNA modifications by mutational profiling sequencing Christel Enroth, Line Dahl Poulsen, Søren Iversen, Finn Kirpekar, Anders Albrechtsen (https://academic.oup.com/nar/article/47/20/e126/5557728) CRISPR/dual-FRET molecular beacon for sensitive live-cell imaging of non-repetitive genomic loci Shiqi Mao, Yachen Ying, Xiaotian Wu, Christopher J Krueger, Antony K Chen (https://academic.oup.com/nar/article/47/20/e131/5557730) Machine learning-based chemical binding similarity using evolutionary relationships of target genes Keunwan Park, Young-Joon Ko, Prasannavenkatesh Durai, Cheol-Ho Pan (https://academic.oup.com/nar/article/47/20/e128/5557731) Robust gene expression control in human cells with a novel universal TetR aptamer splicing module Adam A Mol, Florian Groher, Britta Schreiber, Ciaran Rühmkorff, Beatrix Suess (https://academic.oup.com/nar/article/47/20/e132/5558126) Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA Jin Wang, Bing Liang Alvin Chew, Yong Lai, Hongping Dong, Luang Xu (https://academic.oup.com/nar/article/47/20/e130/5558129) A general LC-MS-based RNA sequencing method for direct analysis of multiple-base modifications in RNA mixtures Ning Zhang, Shundi Shi, Tony Z Jia, Ashley Ziegler, Barney Yoo (https://academic.oup.com/nar/article/47/20/e125/5558343) BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches Bin Liu, Xin Gao, Hanyu Zhang (https://academic.oup.com/nar/article/47/20/e127/5559689) Dynamics of the DEAD-box ATPase Prp5 RecA-like domains provide a conformational switch during spliceosome assembly David H Beier, Tucker J Carrocci, Clarisse van der Feltz, U Sandy Tretbar, Joshua C Paulson (https://academic.oup.com/nar/article/47/20/10842/5563948) Kinetic and subcellular analysis of PS-ASO/protein interactions with P54nrb and RNase H1 Timothy A Vickers, Meghdad Rahdar, Thazha P Prakash, Stanley T Crooke (https://academic.oup.com/nar/article/47/20/10865/5565286) CSB interacts with BRCA1 in late S/G2 to promote MRN- and CtIP-mediated DNA end resection Nicole L Batenburg, John R Walker, Yan Coulombe, Alana Sherker, Jean-Yves Masson (https://academic.oup.com/nar/article/47/20/10678/5566585) Training-free measures based on algorithmic probability identify high nucleosome occupancy in DNA sequences Hector Zenil, Peter Minary (https://academic.oup.com/nar/article/47/20/e129/5568206) Stage-specific combinations of opposing poly(A) modifying enzymes guide gene expression during early oogenesis Marco Nousch, Assa Yeroslaviz, Christian R Eckmann (https://academic.oup.com/nar/article/47/20/10881/5568212) At least two molecules of the RNA helicase Has1 are simultaneously present in pre-ribosomes during ribosome biogenesis Sivakumar Vadivel Gnanasundram, Isabelle C Kos-Braun, Martin Koš (https://academic.oup.com/nar/article/47/20/10852/5568215) Phosphorylation of Drosophila CENP-A on serine 20 regulates protein turn-over and centromere-specific loading Anming Huang, Leopold Kremser, Fabian Schuler, Doris Wilflingseder, Herbert Lindner (https://academic.oup.com/nar/article/47/20/10754/5571580) iRAPs curb antisense transcription in E. coli Andrés Magán, Fabian Amman, Fatinah El-Isa, Natascha Hartl, Ilya Shamovsky (https://academic.oup.com/nar/article/47/20/10894/5571581) A polar filter in DNA polymerases prevents ribonucleotide incorporation Mary K Johnson, Jithesh Kottur, Deepak T Nair (https://academic.oup.com/nar/article/47/20/10693/5572565) Quantifying the impact of small molecule ligands on G-quadruplex stability against Bloom helicase Parastoo Maleki, Golam Mustafa, Prabesh Gyawali, Jagat B Budhathoki, Yue Ma (https://academic.oup.com/nar/article/47/20/10744/5572569) PP4 phosphatase cooperates in recombinational DNA repair by enhancing double-strand break end resection María Teresa Villoria, Pilar Gutiérrez-Escribano, Esmeralda Alonso-Rodríguez, Facundo Ramos, Eva Merino (https://academic.oup.com/nar/article/47/20/10706/5572570) Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase Timothy D Craggs, Marko Sustarsic, Anne Plochowietz, Majid Mosayebi, Hendrik Kaju (https://academic.oup.com/nar/article/47/20/10788/5572571) Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification Gabriel E Hoffman, Jaroslav Bendl, Kiran Girdhar, Eric E Schadt, Panos Roussos (https://academic.oup.com/nar/article/47/20/10597/5572574) RNA binding candidates for human ADAR3 from substrates of a gain of function mutant expressed in neuronal cells Yuru Wang, Dong hee Chung, Leanna R Monteleone, Jie Li, Yao Chiang (https://academic.oup.com/nar/article/47/20/10801/5573551) Cell-free expression of RNA encoded genes using MS2 replicase Laura I Weise, Michael Heymann, Viktoria Mayr, Hannes Mutschler (https://academic.oup.com/nar/article/47/20/10956/5576120) AID--RNA polymerase II transcription-dependent deamination of IgV DNA Phuong Pham, Sohail Malik, Chiho Mak, Peter C Calabrese, Robert G Roeder (https://academic.oup.com/nar/article/47/20/10815/5576121) Structural insights into synthetic ligands targeting A--A pairs in disease-related CAG RNA repeats Sanjukta Mukherjee, Leszek Błaszczyk, Wojciech Rypniewski, Christoph Falschlunger, Ronald Micura (https://academic.oup.com/nar/article/47/20/10906/5576126) Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes Alexander Donath, Frank Jühling, Marwa Al-Arab, Stephan H Bernhart, Franziska Reinhardt (https://academic.oup.com/nar/article/47/20/10543/5580899) Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data Karl J V Nordström, Florian Schmidt, Nina Gasparoni, Abdulrahman Salhab, Gilles Gasparoni (https://academic.oup.com/nar/article/47/20/10580/5580902) Thermal cycling of DNA devices via associative strand displacement Jaeseung Hahn, William M Shih (https://academic.oup.com/nar/article/47/20/10968/5580905) Targeted live-cell nuclear delivery of the DNA 'light-switching' Ru(II) complex via ion-pairing with chlorophenolate counter-anions: the critical role of binding stability and lipophilicity of the ion-pairing complexes Xi-Juan Chao, Miao Tang, Rong Huang, Chun-Hua Huang, Jie Shao (https://academic.oup.com/nar/article/47/20/10520/5580907) New substituted quinoxalines inhibit triple-negative breast cancer by specifically downregulating the c-MYC transcription Ming-Hao Hu, Tian-Ying Wu, Qiong Huang, Guangyi Jin (https://academic.oup.com/nar/article/47/20/10529/5580910) Synonymous genome recoding: a tool to explore microbial biology and new therapeutic strategies Miguel Angel Martínez, Ana Jordan-Paiz, Sandra Franco, Maria Nevot (https://academic.oup.com/nar/article/47/20/10506/5580912) SINEUP non-coding RNAs rescue defective frataxin expression and activity in a cellular model of Friedreich's Ataxia Carlotta Bon, Riccardo Luffarelli, Roberta Russo, Silvia Fortuni, Bianca Pierattini (https://academic.oup.com/nar/article/47/20/10728/5580914) Structure and function of the Toscana virus cap-snatching endonuclease Rhian Jones, Sana Lessoued, Kristina Meier, Stéphanie Devignot, Sergio Barata-García (https://academic.oup.com/nar/article/47/20/10914/5580917) A global functional analysis of missense mutations reveals two major hotspots in the PALB2 tumor suppressor Amélie Rodrigue, Guillaume Margaillan, Thiago Torres Gomes, Yan Coulombe, Gemma Montalban (https://academic.oup.com/nar/article/47/20/10662/5581727) Histone deacetylase 3 controls a transcriptional network required for B cell maturation Kristy R Stengel, Srividya Bhaskara, Jing Wang, Qi Liu, Jacob D Ellis (https://academic.oup.com/nar/article/47/20/10612/5581732) Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition Akira Hirata, Keisuke Okada, Kazuaki Yoshii, Hiroyuki Shiraishi, Shinya Saijo (https://academic.oup.com/nar/article/47/20/10942/5581736) The glucocorticoid receptor interferes with progesterone receptor-dependent genomic regulation in breast cancer cells Maria F Ogara, Santiago A Rodríguez-Seguí, Melisa Marini, Ana Silvina Nacht, Martin Stortz (https://academic.oup.com/nar/article/47/20/10645/5584522) Bacterial cell cycle and growth phase switch by the essential transcriptional regulator CtrA Marie Delaby, Gaël Panis, Patrick H Viollier (https://academic.oup.com/nar/article/47/20/10628/5584559) Star-PAP controlled alternative polyadenylation coupled poly(A) tail length regulates protein expression in hypertrophic heart A P Sudheesh, Nimmy Mohan, Nimmy Francis, Rakesh S Laishram, Richard A Anderson (https://academic.oup.com/nar/article/47/20/10771/5584578) Structural basis for 2'-deoxyguanosine recognition by the 2'-dG-II class of riboswitches Michal M Matyjasik, Robert T Batey (https://academic.oup.com/nar/article/47/20/10931/5584659) Systematic search for structural motifs of peptide binding to double-stranded DNA Nina Kolchina, Vladimir Khavinson, Natalia Linkova, Alexander Yakimov, Dmitry Baitin (https://academic.oup.com/nar/article/47/20/10553/5584680) Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria William D Baez, Bappaditya Roy, Zakkary A McNutt, Elan A Shatoff, Shicheng Chen (https://academic.oup.com/nar/article/47/20/10477/5584838) Understanding the binding specificities of mRNA targets by the mammalian Quaking protein Monika Sharma, Shakshi Sharma, Apoorv Alawada (https://academic.oup.com/nar/article/47/20/10564/5585548) Modifying a covarying protein--DNA interaction changes substrate preference of a site-specific endonuclease Marc Laforet, Thomas A McMurrough, Michael Vu, Christopher M Brown, Kun Zhang (https://academic.oup.com/nar/article/47/20/10830/5585550) Unsubscribe (http://cp20.com/unsubscribe) Manage email alerts (https://academic.oup.com/my-account/email-alerts) Written requests to unsubscribe can be sent to: Journals Marketing, Oxford University Press, Great Clarendon Street, Oxford, 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New issue alert
 
 
 
 
NAR Cancer is now accepting submissions!
 
New Open Access journal NAR Cancer publishes original research, Survey and Summary articles at the intersection of the nucleic acids research and cancer fields, including cancer computational biology and data resources, DNA damage sensing and repair, gene regulation and chromatin, genomics, methods, nucleic acid-based therapeutics, and structural biology. Submit your research.
 
 
 
 
 
 
Nucleic Acids Research  
Volume 47 Issue 20
 
18 November 2019
 
button-issue.png
 
 
 
DNA nanotechnology approaches for microRNA detection and diagnosis border= 
 
Arun Richard Chandrasekaran ; Jibin Abraham Punnoose; Lifeng Zhou; Paromita Dey; Bijan K Dey ...
 
 
 
 
iDamage: a method to integrate modified DNA into the yeast genome border= 
 
Katarzyna H Masłowska ; Luisa Laureti; Vincent Pagès
 
 
 
 
Ularcirc: visualization and enhanced analysis of circular RNAs via back and canonical forward splicing border= 
 
David T Humphreys ; Nicolas Fossat; Madeleine Demuth; Patrick P L Tam; Joshua W K Ho
 
 
 
 
Detection of internal N7-methylguanosine (m7 G) RNA modifications by mutational profiling sequencing border= 
 
Christel Enroth; Line Dahl Poulsen; Søren Iversen; Finn Kirpekar; Anders Albrechtsen ...
 
 
 
 
CRISPR/dual-FRET molecular beacon for sensitive live-cell imaging of non-repetitive genomic loci border= 
 
Shiqi Mao ; Yachen Ying; Xiaotian Wu; Christopher J Krueger; Antony K Chen
 
 
 
 
Machine learning-based chemical binding similarity using evolutionary relationships of target genes border= 
 
Keunwan Park ; Young-Joon Ko; Prasannavenkatesh Durai; Cheol-Ho Pan
 
 
 
 
Robust gene expression control in human cells with a novel universal TetR aptamer splicing module border= 
 
Adam A Mol ; Florian Groher; Britta Schreiber; Ciaran Rühmkorff; Beatrix Suess
 
 
 
 
Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA border= 
 
Jin Wang ; Bing Liang Alvin Chew; Yong Lai; Hongping Dong; Luang Xu ...
 
 
 
 
A general LC-MS-based RNA sequencing method for direct analysis of multiple-base modifications in RNA mixtures border= 
 
Ning Zhang ; Shundi Shi; Tony Z Jia; Ashley Ziegler; Barney Yoo ...
 
 
 
 
BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches border= 
 
Bin Liu ; Xin Gao; Hanyu Zhang
 
 
 
 
Dynamics of the DEAD-box ATPase Prp5 RecA-like domains provide a conformational switch during spliceosome assembly border= 
 
David H Beier ; Tucker J Carrocci; Clarisse van der Feltz; U Sandy Tretbar; Joshua C Paulson ...
 
 
 
 
Kinetic and subcellular analysis of PS-ASO/protein interactions with P54nrb and RNase H1 border= 
 
Timothy A Vickers ; Meghdad Rahdar; Thazha P Prakash; Stanley T Crooke
 
 
 
 
CSB interacts with BRCA1 in late S/G2 to promote MRN- and CtIP-mediated DNA end resection border= 
 
Nicole L Batenburg ; John R Walker; Yan Coulombe; Alana Sherker; Jean-Yves Masson ...
 
 
 
 
Training-free measures based on algorithmic probability identify high nucleosome occupancy in DNA sequences border= 
 
Hector Zenil ; Peter Minary
 
 
 
 
Stage-specific combinations of opposing poly(A) modifying enzymes guide gene expression during early oogenesis border= 
 
Marco Nousch ; Assa Yeroslaviz; Christian R Eckmann
 
 
 
 
At least two molecules of the RNA helicase Has1 are simultaneously present in pre-ribosomes during ribosome biogenesis border= 
 
Sivakumar Vadivel Gnanasundram ; Isabelle C Kos-Braun; Martin Koš
 
 
 
 
Phosphorylation of Drosophila CENP-A on serine 20 regulates protein turn-over and centromere-specific loading border= 
 
Anming Huang ; Leopold Kremser; Fabian Schuler; Doris Wilflingseder; Herbert Lindner ...
 
 
 
 
iRAPs curb antisense transcription in E. coli  border= 
 
Andrés Magán; Fabian Amman ; Fatinah El-Isa; Natascha Hartl; Ilya Shamovsky ...
 
 
 
 
A polar filter in DNA polymerases prevents ribonucleotide incorporation border= 
 
Mary K Johnson ; Jithesh Kottur; Deepak T Nair
 
 
 
 
Quantifying the impact of small molecule ligands on G-quadruplex stability against Bloom helicase border= 
 
Parastoo Maleki ; Golam Mustafa; Prabesh Gyawali; Jagat B Budhathoki; Yue Ma ...
 
 
 
 
PP4 phosphatase cooperates in recombinational DNA repair by enhancing double-strand break end resection border= 
 
María Teresa Villoria ; Pilar Gutiérrez-Escribano; Esmeralda Alonso-Rodríguez; Facundo Ramos; Eva Merino ...
 
 
 
 
Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase border= 
 
Timothy D Craggs ; Marko Sustarsic; Anne Plochowietz; Majid Mosayebi; Hendrik Kaju ...
 
 
 
 
Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification border= 
 
Gabriel E Hoffman ; Jaroslav Bendl; Kiran Girdhar; Eric E Schadt; Panos Roussos
 
 
 
 
RNA binding candidates for human ADAR3 from substrates of a gain of function mutant expressed in neuronal cells border= 
 
Yuru Wang ; Dong hee Chung; Leanna R Monteleone; Jie Li; Yao Chiang ...
 
 
 
 
Cell-free expression of RNA encoded genes using MS2 replicase border= 
 
Laura I Weise; Michael Heymann; Viktoria Mayr; Hannes Mutschler
 
 
 
 
AID'RNA polymerase II transcription-dependent deamination of IgV DNA border= 
 
Phuong Pham ; Sohail Malik; Chiho Mak; Peter C Calabrese; Robert G Roeder ...
 
 
 
 
Structural insights into synthetic ligands targeting A'A pairs in disease-related CAG RNA repeats border= 
 
Sanjukta Mukherjee ; Leszek Błaszczyk; Wojciech Rypniewski; Christoph Falschlunger; Ronald Micura ...
 
 
 
 
Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes border= 
 
Alexander Donath ; Frank Jühling; Marwa Al-Arab; Stephan H Bernhart; Franziska Reinhardt ...
 
 
 
 
Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data border= 
 
Karl J V Nordström ; Florian Schmidt; Nina Gasparoni; Abdulrahman Salhab; Gilles Gasparoni ...
 
 
 
 
Thermal cycling of DNA devices via associative strand displacement border= 
 
Jaeseung Hahn ; William M Shih
 
 
 
 
Targeted live-cell nuclear delivery of the DNA light-switching' Ru(II) complex via ion-pairing with chlorophenolate counter-anions: the critical role of binding stability and lipophilicity of the ion-pairing complexes border= 
 
Xi-Juan Chao ; Miao Tang; Rong Huang; Chun-Hua Huang; Jie Shao ...
 
 
 
 
New substituted quinoxalines inhibit triple-negative breast cancer by specifically downregulating the c-MYC transcription border= 
 
Ming-Hao Hu; Tian-Ying Wu ; Qiong Huang; Guangyi Jin
 
 
 
 
Synonymous genome recoding: a tool to explore microbial biology and new therapeutic strategies border= 
 
Miguel Angel Martínez ; Ana Jordan-Paiz; Sandra Franco; Maria Nevot
 
 
 
 
SINEUP non-coding RNAs rescue defective frataxin expression and activity in a cellular model of Friedreich's Ataxia border= 
 
Carlotta Bon ; Riccardo Luffarelli; Roberta Russo; Silvia Fortuni; Bianca Pierattini ...
 
 
 
 
Structure and function of the Toscana virus cap-snatching endonuclease border= 
 
Rhian Jones ; Sana Lessoued; Kristina Meier; Stéphanie Devignot; Sergio Barata-García ...
 
 
 
 
A global functional analysis of missense mutations reveals two major hotspots in the PALB2 tumor suppressor border= 
 
Amélie Rodrigue; Guillaume Margaillan ; Thiago Torres Gomes; Yan Coulombe; Gemma Montalban ...
 
 
 
 
Histone deacetylase 3 controls a transcriptional network required for B cell maturation border= 
 
Kristy R Stengel ; Srividya Bhaskara; Jing Wang; Qi Liu; Jacob D Ellis ...
 
 
 
 
Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition border= 
 
Akira Hirata ; Keisuke Okada; Kazuaki Yoshii; Hiroyuki Shiraishi; Shinya Saijo ...
 
 
 
 
The glucocorticoid receptor interferes with progesterone receptor-dependent genomic regulation in breast cancer cells border= 
 
Maria F Ogara ; Santiago A Rodríguez-Seguí; Melisa Marini; Ana Silvina Nacht; Martin Stortz ...
 
 
 
 
Bacterial cell cycle and growth phase switch by the essential transcriptional regulator CtrA border= 
 
Marie Delaby ; Gaël Panis; Patrick H Viollier
 
 
 
 
Star-PAP controlled alternative polyadenylation coupled poly(A) tail length regulates protein expression in hypertrophic heart border= 
 
A P Sudheesh ; Nimmy Mohan; Nimmy Francis; Rakesh S Laishram; Richard A Anderson
 
 
 
 
Structural basis for 2-deoxyguanosine recognition by the 2-dG-II class of riboswitches border= 
 
Michal M Matyjasik ; Robert T Batey
 
 
 
 
Systematic search for structural motifs of peptide binding to double-stranded DNA border= 
 
Nina Kolchina ; Vladimir Khavinson; Natalia Linkova; Alexander Yakimov; Dmitry Baitin ...
 
 
 
 
Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria border= 
 
William D Baez; Bappaditya Roy; Zakkary A McNutt; Elan A Shatoff; Shicheng Chen ...
 
 
 
 
Understanding the binding specificities of mRNA targets by the mammalian Quaking protein border= 
 
Monika Sharma ; Shakshi Sharma; Apoorv Alawada
 
 
 
 
Modifying a covarying protein'DNA interaction changes substrate preference of a site-specific endonuclease border= 
 
Marc Laforet ; Thomas A McMurrough; Michael Vu; Christopher M Brown; Kun Zhang ...
 
 
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