Subject: Nucleic Acids Research Table of Contents for 10 January 2020 ------=_Part_1082863955.1578617304178 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** Nucleic Acids Research *** Volume 48, Issue 1, 10 January 2020 Read this issue (https://academic.oup.com/nar/issue/48/1) ------------------------------ 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. ------------------------------ ============================= Survey and Summary ============================A guide to computational methods for G-quadruplex prediction Emilia Puig Lombardi, Arturo Londoño-Vallejo (https://academic.oup.com/nar/article/48/1/1/5637585) Multiple roles of DNA2 nuclease/helicase in DNA metabolism, genome stability and human diseases Li Zheng, Yuan Meng, Judith L Campbell, Binghui Shen (https://academic.oup.com/nar/article/48/1/16/5637586) ============================= Chemical Biology and Nucleic Acid Chemistry ============================Potent and sustained huntingtin lowering via AAV5 encoding miRNA preserves striatal volume and cognitive function in a humanized mouse model of Huntington disease Nicholas S Caron, Amber L Southwell, Cynthia C Brouwers, Louisa Dal Cengio, Yuanyun Xie (https://academic.oup.com/nar/article/48/1/36/5634035) Epigenetic modification of cytosines fine tunes the stability of i-motif DNA Elisé P Wright, Mahmoud A S Abdelhamid, Michelle O Ehiabor, Melanie C Grigg, Kelly Irving (https://academic.oup.com/nar/article/48/1/55/5644997) In vitro and in vivo properties of therapeutic oligonucleotides containing non-chiral 3' and 5' thiophosphate linkages Jörg Duschmalé, Henrik Frydenlund Hansen, Martina Duschmalé, Erich Koller, Nanna Albaek (https://academic.oup.com/nar/article/48/1/63/5637591) Targeted delivery and enhanced gene-silencing activity of centrally modified folic acid--siRNA conjugates Lidya Salim, Golam Islam, Jean-Paul Desaulniers (https://academic.oup.com/nar/article/48/1/75/5644999) ============================= Computational Biology ============================SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble Ruth Huh, Yuchen Yang, Yuchao Jiang, Yin Shen, Yun Li (https://academic.oup.com/nar/article/48/1/86/5644992) ============================= Data Resources and Analyses ============================PRMT1-mediated methylation of the microprocessor-associated proteins regulates microRNA biogenesis Valeria Spadotto, Roberto Giambruno, Enrico Massignani, Marija Mihailovich, Marianna Maniaci (https://academic.oup.com/nar/article/48/1/96/5645000) ============================= Gene Regulation, Chromatin and Epigenetics ============================ILF3 contributes to the establishment of the antiviral type I interferon program Samir F Watson, Nicolas Bellora, Sara Macias (https://academic.oup.com/nar/article/48/1/116/5614571) Targeted PMP22 TATA-box editing by CRISPR/Cas9 reduces demyelinating neuropathy of Charcot-Marie-Tooth disease type 1A in mice Ji-Su Lee, Jae Y Lee, Dong W Song, Hee S Bae, Hyun M Doo (https://academic.oup.com/nar/article/48/1/130/5622709) Nuclear Ccr4-Not mediates the degradation of telomeric and transposon transcripts at chromatin in the Drosophila germline Maria Kordyukova, Olesya Sokolova, Valeriya Morgunova, Sergei Ryazansky, Natalia Akulenko (https://academic.oup.com/nar/article/48/1/141/5625537) The histone variant H2A.Z in yeast is almost exclusively incorporated into the +1 nucleosome in the direction of transcription Dia N Bagchi, Anna M Battenhouse, Daechan Park, Vishwanath R Iyer (https://academic.oup.com/nar/article/48/1/157/5624977) Global H-NS counter-silencing by LuxR activates quorum sensing gene expression Ryan R Chaparian, Minh L N Tran, Laura C Miller Conrad, Douglas B Rusch, Julia C van Kessel (https://academic.oup.com/nar/article/48/1/171/5634033) Discovery of a new predominant cytosine DNA modification that is linked to gene expression in malaria parasites Elie Hammam, Guruprasad Ananda, Ameya Sinha, Christine Scheidig-Benatar, Mylene Bohec (https://academic.oup.com/nar/article/48/1/184/5644996) ============================= Genome Integrity, Repair and Replication ============================A nucleotide-dependent oligomerization of the Escherichia coli replication initiator DnaA requires residue His136 for remodeling of the chromosomal origin Rahul Saxena, Christopher B Stanley, Pankaj Kumar, Matthew J Cuneo, Digvijay Patil (https://academic.oup.com/nar/article/48/1/200/5608987) Frequent template switching in postreplication gaps: suppression of deleterious consequences by the Escherichia coli Uup and RadD proteins Zachary J Romero, Thomas J Armstrong, Sarah S Henrikus, Stefanie H Chen, David J Glass (https://academic.oup.com/nar/article/48/1/212/5609528) Transcription-coupled nucleotide excision repair is coordinated by ubiquitin and SUMO in response to ultraviolet irradiation Frauke Liebelt, Joost Schimmel, Matty Verlaan -- de Vries, Esra Klemann, Martin E van Royen (https://academic.oup.com/nar/article/48/1/231/5624976) Genome replication dynamics of a bacteriophage and its satellite reveal strategies for parasitism and viral restriction Zachary K Barth, Tania V Silvas, Angus Angermeyer, Kimberley D Seed (https://academic.oup.com/nar/article/48/1/249/5610345) Inactivation of folylpolyglutamate synthetase Met7 results in genome instability driven by an increased dUTP/dTTP ratio Tobias T Schmidt, Sushma Sharma, Gloria X Reyes, Anna Kolodziejczak, Tina Wagner (https://academic.oup.com/nar/article/48/1/264/5606628) ============================= Genomics ============================Exploring trophoblast-specific Tead4 enhancers through chromatin conformation capture assays followed by functional screening Junko Tomikawa, Shuji Takada, Kohji Okamura, Miho Terao, Hiroko Ogata-Kawata (https://academic.oup.com/nar/article/48/1/278/5644998) Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster Christopher E Ellison, Weihuan Cao (https://academic.oup.com/nar/article/48/1/290/5637587) ============================= Molecular Biology ============================A double-stranded RNA platform is required for the interaction between a host restriction factor and the NS1 protein of influenza A virus Guifang Chen, Li-Chung Ma, Shanshan Wang, Ryan L Woltz, Emily M Grasso (https://academic.oup.com/nar/article/48/1/304/5637589) A single amino acid switch converts the Sleeping Beauty transposase into an efficient unidirectional excisionase with utility in stem cell reprogramming Lisa Kesselring, Csaba Miskey, Cecilia Zuliani, Irma Querques, Vladimir Kapitonov (https://academic.oup.com/nar/article/48/1/316/5644994) ============================= Nucleic Acid Enzymes ============================Sinorhizobium meliloti YbeY is a zinc-dependent single-strand specific endoribonuclease that plays an important role in 16S ribosomal RNA processing Vignesh M P Babu, Siva Sankari, James A Budnick, Clayton C Caswell, Graham C Walker (https://academic.oup.com/nar/article/48/1/332/5645002) A novel 5'-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes Selom K Doamekpor, Agnieszka Gozdek, Aleksandra Kwasnik, Joanna Kufel, Liang Tong (https://academic.oup.com/nar/article/48/1/349/5645008) ============================= RNA and RNA-protein complexes ============================RbfA and IF3 couple ribosome biogenesis and translation initiation to increase stress tolerance Indra Mani Sharma, Sarah A Woodson (https://academic.oup.com/nar/article/48/1/359/5625924) Structural transitions in the RNA 7SK 5' hairpin and their effect on HEXIM binding Konstantin Röder, Guillaume Stirnemann, Anne-Catherine Dock-Bregeon, David J Wales, Samuela Pasquali (https://academic.oup.com/nar/article/48/1/373/5626526) A unique internal ribosome entry site representing a dynamic equilibrium state of RNA tertiary structure in the 5'-UTR of Wheat yellow mosaic virus RNA1 Guowei Geng, Chengming Yu, Xiangdong Li, Xuefeng Yuan (https://academic.oup.com/nar/article/48/1/390/5622710) Pol5 is required for recycling of small subunit biogenesis factors and for formation of the peptide exit tunnel of the large ribosomal subunit Christina M Braun, Philipp Hackert, Catharina E Schmid, Markus T Bohnsack, Katherine E Bohnsack (https://academic.oup.com/nar/article/48/1/405/5634039) ============================= Structural Biology ============================A non-canonical monovalent zinc finger stabilizes the integration of Cfp1 into the H3K4 methyltransferase complex COMPASS Yidai Yang, Monika Joshi, Yoh-hei Takahashi, Zhibin Ning, Qianhui Qu (https://academic.oup.com/nar/article/48/1/421/5625525) Structural insight into the length-dependent binding of ssDNA by SP_0782 from Streptococcus pneumoniae, reveals a divergence in the DNA-binding interface of PC4-like proteins Shuangli Li, Guoliang Lu, Xiang Fang, Theresa A Ramelot, Michael A Kennedy (https://academic.oup.com/nar/article/48/1/432/5622711) 'Drc', a structurally novel ssDNA-binding transcription regulator of N4-related bacterial viruses Maarten Boon, Elke De Zitter, Jeroen De Smet, Jeroen Wagemans, Marleen Voet (https://academic.oup.com/nar/article/48/1/445/5625530) Structural insights into target DNA recognition by R2R3-MYB transcription factors Baihui Wang, Qiang Luo, Yingping Li, Liufan Yin, Nana Zhou (https://academic.oup.com/nar/article/48/1/460/5626523) ============================= Synthetic Biology and Bioengineering ============================A heterodimer of evolved designer-recombinases precisely excises a human genomic DNA locus Felix Lansing, Maciej Paszkowski-Rogacz, Lukas Theo Schmitt, Paul Martin Schneider, Teresa Rojo Romanos (https://academic.oup.com/nar/article/48/1/472/5634038) Phylogenetic debugging of a complete human biosynthetic pathway transplanted into yeast Neta Agmon, Jasmine Temple, Zuojian Tang, Tobias Schraink, Maayan Baron (https://academic.oup.com/nar/article/48/1/486/5634032) ============================= Corrigendum ============================Crystal structure of the N-terminal domain of human Timeless and its interaction with Tipin Sandro Holzer, Gianluca Degliesposti, Mairi L Kilkenny, Sarah L Maslen, Dijana Matak-Vinkovíc (https://academic.oup.com/nar/article/48/1/500/5637583) ============================= Methods Online ============================An improved platform for functional assessment of large protein libraries in mammalian cells Kenneth A Matreyek, Jason J Stephany, Melissa A Chiasson, Nicholas Hasle, Douglas M Fowler (https://academic.oup.com/nar/article/48/1/e1/5587635) Gene knockdown in malaria parasites via non-canonical RNAi Franziska Hentzschel, Vera Mitesser, Sabine Anne-Kristin Fraschka, Daria Krzikalla, Elena Herrera Carrillo (https://academic.oup.com/nar/article/48/1/e2/5611670) Evolution-guided engineering of small-molecule biosensors Tim Snoek, Evan K Chaberski, Francesca Ambri, Stefan Kol, Sara P Bjørn (https://academic.oup.com/nar/article/48/1/e3/5645005) FIN-Seq: transcriptional profiling of specific cell types from frozen archived tissue of the human central nervous system Ryoji Amamoto, Emanuela Zuccaro, Nathan C Curry, Sonia Khurana, Hsu-Hsin Chen (https://academic.oup.com/nar/article/48/1/e4/5625923) A general strategy exploiting m5C duplex-remodelling effect for selective detection of RNA and DNA m5C methyltransferase activity in cells Tianming Yang, Joanne J A Low, Esther C Y Woon (https://academic.oup.com/nar/article/48/1/e5/5613678) An in vitro single-molecule assay for eukaryotic cap-dependent translation initiation kinetics Hongyun Wang, Lexi Sun, Anthony Gaba, Xiaohui Qu (https://academic.oup.com/nar/article/48/1/e6/5624971) 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, OX2 6DP, UK. Our Privacy Policy (http://global.oup.com/privacy) sets out how Oxford University Press handles your personal information. The content of this email is protected by copyright. Oxford University Press This email is intended for bionet@evol.mcmaster.ca. ------=_Part_1082863955.1578617304178 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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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 48 Issue 1
 
10 January 2020
 
button-issue.png
 
 
Survey and Summary
 
 
 
A guide to computational methods for G-quadruplex prediction border= 
 
Emilia Puig Lombardi ; Arturo Londoño-Vallejo
 
 
Multiple roles of DNA2 nuclease/helicase in DNA metabolism, genome stability and human diseases border= 
 
Li Zheng ; Yuan Meng; Judith L Campbell; Binghui Shen
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Potent and sustained huntingtin lowering via AAV5 encoding miRNA preserves striatal volume and cognitive function in a humanized mouse model of Huntington disease border= 
 
Nicholas S Caron ; Amber L Southwell; Cynthia C Brouwers; Louisa Dal Cengio; Yuanyun Xie ...
 
 
Epigenetic modification of cytosines fine tunes the stability of i-motif DNA border= 
 
Elisé P Wright ; Mahmoud A S Abdelhamid; Michelle O Ehiabor; Melanie C Grigg; Kelly Irving ...
 
 
In vitro and in vivo properties of therapeutic oligonucleotides containing non-chiral 3 and 5 thiophosphate linkages border= 
 
Jörg Duschmalé ; Henrik Frydenlund Hansen; Martina Duschmalé; Erich Koller; Nanna Albaek ...
 
 
Targeted delivery and enhanced gene-silencing activity of centrally modified folic acid'siRNA conjugates border= 
 
Lidya Salim ; Golam Islam; Jean-Paul Desaulniers
 
 
 
Computational Biology
 
 
 
SAME-clustering: Single-cell Aggregated Clustering via M ixture Model Ensemble border= 
 
Ruth Huh; Yuchen Yang ; Yuchao Jiang; Yin Shen; Yun Li
 
 
 
Data Resources and Analyses
 
 
 
PRMT1-mediated methylation of the microprocessor-associated proteins regulates microRNA biogenesis border= 
 
Valeria Spadotto ; Roberto Giambruno; Enrico Massignani; Marija Mihailovich; Marianna Maniaci ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
ILF3 contributes to the establishment of the antiviral type I interferon program border= 
 
Samir F Watson ; Nicolas Bellora; Sara Macias
 
 
Targeted PMP22 TATA-box editing by CRISPR/Cas9 reduces demyelinating neuropathy of Charcot-Marie-Tooth disease type 1A in mice border= 
 
Ji-Su Lee ; Jae Y Lee; Dong W Song; Hee S Bae; Hyun M Doo ...
 
 
Nuclear Ccr4-Not mediates the degradation of telomeric and transposon transcripts at chromatin in the Drosophila germline border= 
 
Maria Kordyukova; Olesya Sokolova ; Valeriya Morgunova; Sergei Ryazansky; Natalia Akulenko ...
 
 
The histone variant H2A.Z in yeast is almost exclusively incorporated into the +1 nucleosome in the direction of transcription border= 
 
Dia N Bagchi ; Anna M Battenhouse; Daechan Park; Vishwanath R Iyer
 
 
Global H-NS counter-silencing by LuxR activates quorum sensing gene expression border= 
 
Ryan R Chaparian ; Minh L N Tran; Laura C Miller Conrad; Douglas B Rusch; Julia C van Kessel
 
 
Discovery of a new predominant cytosine DNA modification that is linked to gene expression in malaria parasites border= 
 
Elie Hammam ; Guruprasad Ananda; Ameya Sinha; Christine Scheidig-Benatar; Mylene Bohec ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
A nucleotide-dependent oligomerization of the Escherichia coli replication initiator DnaA requires residue His136 for remodeling of the chromosomal origin border= 
 
Rahul Saxena ; Christopher B Stanley; Pankaj Kumar; Matthew J Cuneo; Digvijay Patil ...
 
 
Frequent template switching in postreplication gaps: suppression of deleterious consequences by the Escherichia coli Uup and RadD proteins border= 
 
Zachary J Romero; Thomas J Armstrong ; Sarah S Henrikus; Stefanie H Chen; David J Glass ...
 
 
Transcription-coupled nucleotide excision repair is coordinated by ubiquitin and SUMO in response to ultraviolet irradiation border= 
 
Frauke Liebelt ; Joost Schimmel; Matty Verlaan ' de Vries; Esra Klemann; Martin E van Royen ...
 
 
Genome replication dynamics of a bacteriophage and its satellite reveal strategies for parasitism and viral restriction border= 
 
Zachary K Barth ; Tania V Silvas; Angus Angermeyer; Kimberley D Seed
 
 
Inactivation of folylpolyglutamate synthetase Met7 results in genome instability driven by an increased dUTP/dTTP ratio border= 
 
Tobias T Schmidt ; Sushma Sharma; Gloria X Reyes; Anna Kolodziejczak; Tina Wagner ...
 
 
 
Genomics
 
 
 
Exploring trophoblast-specific Tead4 enhancers through chromatin conformation capture assays followed by functional screening border= 
 
Junko Tomikawa ; Shuji Takada; Kohji Okamura; Miho Terao; Hiroko Ogata-Kawata ...
 
 
Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster  border= 
 
Christopher E Ellison; Weihuan Cao
 
 
 
Molecular Biology
 
 
 
A double-stranded RNA platform is required for the interaction between a host restriction factor and the NS1 protein of influenza A virus border= 
 
Guifang Chen ; Li-Chung Ma; Shanshan Wang; Ryan L Woltz; Emily M Grasso ...
 
 
A single amino acid switch converts the Sleeping Beauty transposase into an efficient unidirectional excisionase with utility in stem cell reprogramming border= 
 
Lisa Kesselring ; Csaba Miskey; Cecilia Zuliani; Irma Querques; Vladimir Kapitonov ...
 
 
 
Nucleic Acid Enzymes
 
 
 
Sinorhizobium meliloti YbeY is a zinc-dependent single-strand specific endoribonuclease that plays an important role in 16S ribosomal RNA processing border= 
 
Vignesh M P Babu ; Siva Sankari; James A Budnick; Clayton C Caswell; Graham C Walker
 
 
A novel 5-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes border= 
 
Selom K Doamekpor ; Agnieszka Gozdek; Aleksandra Kwasnik; Joanna Kufel; Liang Tong
 
 
 
RNA and RNA-protein complexes
 
 
 
RbfA and IF3 couple ribosome biogenesis and translation initiation to increase stress tolerance border= 
 
Indra Mani Sharma ; Sarah A Woodson
 
 
Structural transitions in the RNA 7SK 5 hairpin and their effect on HEXIM binding border= 
 
Konstantin Röder ; Guillaume Stirnemann; Anne-Catherine Dock-Bregeon; David J Wales; Samuela Pasquali
 
 
A unique internal ribosome entry site representing a dynamic equilibrium state of RNA tertiary structure in the 5-UTR of Wheat yellow mosaic virus RNA1 border= 
 
Guowei Geng; Chengming Yu ; Xiangdong Li; Xuefeng Yuan
 
 
Pol5 is required for recycling of small subunit biogenesis factors and for formation of the peptide exit tunnel of the large ribosomal subunit border= 
 
Christina M Braun ; Philipp Hackert; Catharina E Schmid; Markus T Bohnsack; Katherine E Bohnsack ...
 
 
 
Structural Biology
 
 
 
A non-canonical monovalent zinc finger stabilizes the integration of Cfp1 into the H3K4 methyltransferase complex COMPASS border= 
 
Yidai Yang ; Monika Joshi; Yoh-hei Takahashi; Zhibin Ning; Qianhui Qu ...
 
 
Structural insight into the length-dependent binding of ssDNA by SP_0782 from Streptococcus pneumoniae, reveals a divergence in the DNA-binding interface of PC4-like proteins border= 
 
Shuangli Li ; Guoliang Lu; Xiang Fang; Theresa A Ramelot; Michael A Kennedy ...
 
 
Drc', a structurally novel ssDNA-binding transcription regulator of N4-related bacterial viruses border= 
 
Maarten Boon ; Elke De Zitter; Jeroen De Smet; Jeroen Wagemans; Marleen Voet ...
 
 
Structural insights into target DNA recognition by R2R3-MYB transcription factors border= 
 
Baihui Wang ; Qiang Luo; Yingping Li; Liufan Yin; Nana Zhou ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
A heterodimer of evolved designer-recombinases precisely excises a human genomic DNA locus border= 
 
Felix Lansing ; Maciej Paszkowski-Rogacz; Lukas Theo Schmitt; Paul Martin Schneider; Teresa Rojo Romanos ...
 
 
Phylogenetic debugging of a complete human biosynthetic pathway transplanted into yeast border= 
 
Neta Agmon ; Jasmine Temple; Zuojian Tang; Tobias Schraink; Maayan Baron ...
 
 
 
Corrigendum
 
 
 
Crystal structure of the N-terminal domain of human Timeless and its interaction with Tipin border= 
 
Sandro Holzer ; Gianluca Degliesposti; Mairi L Kilkenny; Sarah L Maslen; Dijana Matak-Vinkovíc ...
 
 
 
Methods Online
 
 
 
An improved platform for functional assessment of large protein libraries in mammalian cells border= 
 
Kenneth A Matreyek ; Jason J Stephany; Melissa A Chiasson; Nicholas Hasle; Douglas M Fowler
 
 
Gene knockdown in malaria parasites via non-canonical RNAi border=  
 
Franziska Hentzschel; Vera Mitesser; Sabine Anne-Kristin Fraschka; Daria Krzikalla; Elena Herrera Carrillo ...
 
 
Evolution-guided engineering of small-molecule biosensors border=  
 
Tim Snoek; Evan K Chaberski; Francesca Ambri; Stefan Kol; Sara P Bjørn ...
 
 
FIN-Seq: transcriptional profiling of specific cell types from frozen archived tissue of the human central nervous system border= 
 
Ryoji Amamoto ; Emanuela Zuccaro; Nathan C Curry; Sonia Khurana; Hsu-Hsin Chen ...
 
 
A general strategy exploiting m5C duplex-remodelling effect for selective detection of RNA and DNA m5 C methyltransferase activity in cells border= 
 
Tianming Yang; Joanne J A Low ; Esther C Y Woon
 
 
An in vitro single-molecule assay for eukaryotic cap-dependent translation initiation kinetics border= 
 
Hongyun Wang ; Lexi Sun; Anthony Gaba; Xiaohui Qu
 
 
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