Subject: Nucleic Acids Research Table of Contents for 16 December 2019 ------=_Part_1195551383.1576267511843 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** Nucleic Acids Research *** Volume 47, Issue 22, 16 December 2019 Read this issue (https://academic.oup.com/nar/issue/47/22) ------------------------------ 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 ============================Super-enhancers in transcriptional regulation and genome organization Xi Wang, Murray J Cairns, Jian Yan (https://academic.oup.com/nar/article/47/22/11481/5625531) The changing paradigm of intron retention: regulation, ramifications and recipes Geoffray Monteuuis, Justin J L Wong, Charles G Bailey, Ulf Schmitz, John E J Rasko (https://academic.oup.com/nar/article/47/22/11497/5625532) ============================= Chemical Biology and Nucleic Acid Chemistry ============================Sulfur-centered hemi-bond radicals as active intermediates in S-DNA phosphorothioate oxidation Jialong Jie, Ye Xia, Chun-Hua Huang, Hongmei Zhao, Chunfan Yang (https://academic.oup.com/nar/article/47/22/11514/5625538) A DNA aptamer for binding and inhibition of DNA methyltransferase 1 Linlin Wang, Ju Yong Lee, Linfeng Gao, Jiekai Yin, Yaokai Duan (https://academic.oup.com/nar/article/47/22/11527/5626520) Structure--fluorescence activation relationships of a large Stokes shift fluorogenic RNA aptamer Christian Steinmetzger, Irene Bessi, Ann-Kathrin Lenz, Claudia Höbartner (https://academic.oup.com/nar/article/47/22/11538/5628921) ============================= Computational Biology ============================Retrotransposons spread potential cis-regulatory elements during mammary gland evolution Hidenori Nishihara (https://academic.oup.com/nar/article/47/22/11551/5603223) Causal Inference Engine: a platform for directional gene set enrichment analysis and inference of active transcriptional regulators Saman Farahmand, Corey O'Connor, Jill A Macoska, Kourosh Zarringhalam (https://academic.oup.com/nar/article/47/22/11563/5614570) ============================= Data Resources and Analyses ============================Epigenetic reader complexes of the human malaria parasite, Plasmodium falciparum Wieteke Anna Maria Hoeijmakers, Jun Miao, Sabine Schmidt, Christa Geeke Toenhake, Sony Shrestha (https://academic.oup.com/nar/article/47/22/11574/5625919) ============================= Gene Regulation, Chromatin and Epigenetics ============================Localization of Drosophila CENP-A to non-centromeric sites depends on the NuRD complex Engin Demirdizen, Matthias Spiller-Becker, Arion Förtsch, Alexander Wilhelm, Samuel Corless (https://academic.oup.com/nar/article/47/22/11589/5622714) Targeted DNA methylation of neurodegenerative disease genes via homology directed repair Christopher P Cali, Daniel S Park, Edward B Lee (https://academic.oup.com/nar/article/47/22/11609/5611673) Histone lysine demethylase KDM4B regulates the alternative splicing of the androgen receptor in response to androgen deprivation Lingling Duan, Zhenhua Chen, Jun Lu, Yanping Liang, Ming Wang (https://academic.oup.com/nar/article/47/22/11623/5606619) Incorporation and influence of Leishmania histone H3 in chromatin Mariko Dacher, Hiroaki Tachiwana, Naoki Horikoshi, Tomoya Kujirai, Hiroyuki Taguchi (https://academic.oup.com/nar/article/47/22/11637/5624974) Distinct CoREST complexes act in a cell-type-specific manner Igor Mačinković, Ina Theofel, Tim Hundertmark, Kristina Kovač, Stephan Awe (https://academic.oup.com/nar/article/47/22/11649/5614567) ============================= Genome Integrity, Repair and Replication ============================The unstructured linker arms of MutL enable GATC site incision beyond roadblocks during initiation of DNA mismatch repair Yannicka S N Mardenborough, Katerina Nitsenko, Charlie Laffeber, Camille Duboc, Enes Sahin (https://academic.oup.com/nar/article/47/22/11667/5584546) Recognition and processing of branched DNA substrates by Slx1--Slx4 nuclease Vineet Gaur, Weronika Ziajko, Shivlee Nirwal, Aleksandra Szlachcic, Marta Gapi"ska (https://academic.oup.com/nar/article/47/22/11681/5580900) Recruitment of Rec8, Pds5 and Rad61/Wapl to meiotic homolog pairing, recombination, axis formation and S-phase Soogil Hong, Jeong H Joo, Hyeseon Yun, Nancy Kleckner, Keun P Kim (https://academic.oup.com/nar/article/47/22/11691/5588348) Lamin A/C promotes DNA base excision repair Scott Maynard, Guido Keijzers, Mansour Akbari, Michael Ben Ezra, Arnaldur Hall (https://academic.oup.com/nar/article/47/22/11709/5606629) Human RAD51 paralogue RAD51C fosters repair of alkylated DNA by interacting with the ALKBH3 demethylase Monisha Mohan, Deepa Akula, Arun Dhillon, Arun Goyal, Roy Anindya (https://academic.oup.com/nar/article/47/22/11729/5603225) ============================= Molecular Biology ============================G-quadruplex structures trigger RNA phase separation Yueying Zhang, Minglei Yang, Susan Duncan, Xiaofei Yang, Mahmoud A S Abdelhamid (https://academic.oup.com/nar/article/47/22/11746/5624975) FBXO47 regulates telomere-inner nuclear envelope integration by stabilizing TRF2 during meiosis Rong Hua, Huafang Wei, Chao Liu, Yue Zhang, Siyu Liu (https://academic.oup.com/nar/article/47/22/11755/5625541) A distinct class of eukaryotic MT-A70 methyltransferases maintain symmetric DNA N6-adenine methylation at the ApT dinucleotides as an epigenetic mark associated with transcription Yuanyuan Wang, Yalan Sheng, Yongqiang Liu, Wenxin Zhang, Ting Cheng (https://academic.oup.com/nar/article/47/22/11771/5624968) Deficiency of mitoribosomal S10 protein affects translation and splicing in Arabidopsis mitochondria Malgorzata Kwasniak-Owczarek, Urszula Kazmierczak, Artur Tomal, Pawel Mackiewicz, Hanna Janska (https://academic.oup.com/nar/article/47/22/11790/5626533) ============================= Nucleic Acid Enzymes ============================Loss of the ribosomal RNA methyltransferase NSUN5 impairs global protein synthesis and normal growth Clemens Heissenberger, Lisa Liendl, Fabian Nagelreiter, Yulia Gonskikh, Guohuan Yang (https://academic.oup.com/nar/article/47/22/11807/5624972) Atomic structures of the RNA end-healing 5'-OH kinase and 2',3'-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor Ankan Banerjee, Yehuda Goldgur, Beate Schwer, Stewart Shuman (https://academic.oup.com/nar/article/47/22/11826/5624966) A pre-catalytic non-covalent step governs DNA polymerase beta fidelity Khadijeh S Alnajjar, Ivan S Krylov, Amirsoheil Negahbani, Pouya Haratipour, Boris A Kashemirov (https://academic.oup.com/nar/article/47/22/11839/5626531) ============================= RNA and RNA-protein complexes ============================Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy Alexey A Malygin, Olesya A Krumkacheva, Dmitri M Graifer, Ivan O Timofeev, Anastasia S Ochkasova (https://academic.oup.com/nar/article/47/22/11850/5625535) The mRNA repressor TRIM71 cooperates with Nonsense-Mediated Decay factors to destabilize the mRNA of CDKN1A/p21 Lucia A Torres-Fernández, Bettina Jux, Maximilian Bille, Yasmine Port, Karin Schneider (https://academic.oup.com/nar/article/47/22/11861/5626522) Single molecule analysis of effects of non-canonical guide RNAs and specificity-enhancing mutations on Cas9-induced DNA unwinding Ikenna C Okafor, Digvijay Singh, Yanbo Wang, Minhee Jung, Haobo Wang (https://academic.oup.com/nar/article/47/22/11880/5622707) Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures Benoît Castandet, Arnaud Germain, Amber M Hotto, David B Stern (https://academic.oup.com/nar/article/47/22/11889/5626524) ============================= Structural Biology ============================Phosphorylation orchestrates the structural ensemble of the intrinsically disordered protein HMGA1a and modulates its DNA binding to the NFkappa B promoter Bastian Kohl, Xueyin Zhong, Christian Herrmann, Raphael Stoll (https://academic.oup.com/nar/article/47/22/11906/5538012) A DNA G-quadruplex/i-motif hybrid Betty Chu, Daoning Zhang, Paul J Paukstelis (https://academic.oup.com/nar/article/47/22/11921/5625527) Structures of 1:1 and 2:1 complexes of BMVC and MYC promoter G-quadruplex reveal a mechanism of ligand conformation adjustment for G4-recognition Wenting Liu, Clement Lin, Guanhui Wu, Jixun Dai, Ta-Chau Chang (https://academic.oup.com/nar/article/47/22/11931/5628923) Crystal structure of the EcoKMcrA N-terminal domain (NEco): recognition of modified cytosine bases without flipping Anton Slyvka, Evelina Zagorskait-, Honorata Czapinska, Giedrius Sasnauskas, Matthias Bochtler (https://academic.oup.com/nar/article/47/22/11943/5625526) ============================= Synthetic Biology and Bioengineering ============================Rapid in vitro production of single-stranded DNA Dionis Minev, Richard Guerra, Jocelyn Y Kishi, Cory Smith, Elisha Krieg (https://academic.oup.com/nar/article/47/22/11956/5622713) Design and synthesis of pleated DNA origami nanotubes with adjustable diameters Jonathan F Berengut, Julian C Berengut, Jonathan P K Doye, Domen Prešern, Akihiro Kawamoto (https://academic.oup.com/nar/article/47/22/11963/5625926) ============================= Corrigendum ============================Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins Michiel Vanmeert, Jamoliddin Razzokov, Muhammad Usman Mirza, Stephen D Weeks, Guy Schepers (https://academic.oup.com/nar/article/47/22/11976/5622705) Robustness by intrinsically disordered C-termini and translational readthrough April Snofrid Kleppe, Erich Bornberg-Bauer (https://academic.oup.com/nar/article/47/22/11978/5626527) ============================= Methods Online ============================Latent cellular analysis robustly reveals subtle diversity in large-scale single-cell RNA-seq data Changde Cheng, John Easton, Celeste Rosencrance, Yan Li, Bensheng Ju (https://academic.oup.com/nar/article/47/22/e143/5576119) High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments Flávia S Papini, Mona Seifert, David Dulin (https://academic.oup.com/nar/article/47/22/e144/5580913) Click-encoded rolling FISH for visualizing single-cell RNA polyadenylation and structures Feng Chen, Min Bai, Xiaowen Cao, Yue Zhao, Jing Xue (https://academic.oup.com/nar/article/47/22/e145/5580904) Convolutional neural network model to predict causal risk factors that share complex regulatory features Taeyeop Lee, Min Kyung Sung, Seulkee Lee, Woojin Yang, Jaeho Oh (https://academic.oup.com/nar/article/47/22/e146/5584519) A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment Ka Wai Leong, Fangyan Yu, Viktor A Adalsteinsson, Sarah Reed, Gregory Gydush (https://academic.oup.com/nar/article/47/22/e147/5584521) Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations Noam Harel, Moran Meir, Uri Gophna, Adi Stern (https://academic.oup.com/nar/article/47/22/e148/5608986) 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_1195551383.1576267511843 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 47 Issue 22
 
16 December 2019
 
button-issue.png
 
 
Survey and Summary
 
 
 
Super-enhancers in transcriptional regulation and genome organization border= 
 
Xi Wang ; Murray J Cairns; Jian Yan
 
 
The changing paradigm of intron retention: regulation, ramifications and recipes border= 
 
Geoffray Monteuuis ; Justin J L Wong; Charles G Bailey; Ulf Schmitz; John E J Rasko
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Sulfur-centered hemi-bond radicals as active intermediates in S-DNA phosphorothioate oxidation border= 
 
Jialong Jie ; Ye Xia; Chun-Hua Huang; Hongmei Zhao; Chunfan Yang ...
 
 
A DNA aptamer for binding and inhibition of DNA methyltransferase 1 border= 
 
Linlin Wang ; Ju Yong Lee; Linfeng Gao; Jiekai Yin; Yaokai Duan ...
 
 
Structure'fluorescence activation relationships of a large Stokes shift fluorogenic RNA aptamer border= 
 
Christian Steinmetzger ; Irene Bessi; Ann-Kathrin Lenz; Claudia Höbartner
 
 
 
Computational Biology
 
 
 
Retrotransposons spread potential cis -regulatory elements during mammary gland evolution border= 
 
Hidenori Nishihara
 
 
Causal Inference Engine: a platform for directional gene set enrichment analysis and inference of active transcriptional regulators border= 
 
Saman Farahmand ; Corey O'Connor; Jill A Macoska; Kourosh Zarringhalam
 
 
 
Data Resources and Analyses
 
 
 
Epigenetic reader complexes of the human malaria parasite, Plasmodium falciparum  border= 
 
Wieteke Anna Maria Hoeijmakers; Jun Miao ; Sabine Schmidt; Christa Geeke Toenhake; Sony Shrestha ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Localization of Drosophila CENP-A to non-centromeric sites depends on the NuRD complex border= 
 
Engin Demirdizen ; Matthias Spiller-Becker; Arion Förtsch; Alexander Wilhelm; Samuel Corless ...
 
 
Targeted DNA methylation of neurodegenerative disease genes via homology directed repair border= 
 
Christopher P Cali ; Daniel S Park; Edward B Lee
 
 
Histone lysine demethylase KDM4B regulates the alternative splicing of the androgen receptor in response to androgen deprivation border= 
 
Lingling Duan ; Zhenhua Chen; Jun Lu; Yanping Liang; Ming Wang ...
 
 
Incorporation and influence of Leishmania histone H3 in chromatin border= 
 
Mariko Dacher; Hiroaki Tachiwana ; Naoki Horikoshi; Tomoya Kujirai; Hiroyuki Taguchi ...
 
 
Distinct CoREST complexes act in a cell-type-specific manner border= 
 
Igor Mačinković; Ina Theofel; Tim Hundertmark; Kristina Kovač; Stephan Awe ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
The unstructured linker arms of MutL enable GATC site incision beyond roadblocks during initiation of DNA mismatch repair border= 
 
Yannicka S N Mardenborough ; Katerina Nitsenko; Charlie Laffeber; Camille Duboc; Enes Sahin ...
 
 
Recognition and processing of branched DNA substrates by Slx1'Slx4 nuclease border= 
 
Vineet Gaur ; Weronika Ziajko; Shivlee Nirwal; Aleksandra Szlachcic; Marta Gapi"ska ...
 
 
Recruitment of Rec8, Pds5 and Rad61/Wapl to meiotic homolog pairing, recombination, axis formation and S-phase border= 
 
Soogil Hong ; Jeong H Joo; Hyeseon Yun; Nancy Kleckner; Keun P Kim
 
 
Lamin A/C promotes DNA base excision repair 
 
Scott Maynard; Guido Keijzers; Mansour Akbari ; Michael Ben Ezra; Arnaldur Hall ...
 
 
Human RAD51 paralogue RAD51C fosters repair of alkylated DNA by interacting with the ALKBH3 demethylase border= 
 
Monisha Mohan ; Deepa Akula; Arun Dhillon; Arun Goyal; Roy Anindya
 
 
 
Molecular Biology
 
 
 
G-quadruplex structures trigger RNA phase separation border= 
 
Yueying Zhang; Minglei Yang; Susan Duncan; Xiaofei Yang; Mahmoud A S Abdelhamid ...
 
 
FBXO47 regulates telomere-inner nuclear envelope integration by stabilizing TRF2 during meiosis border= 
 
Rong Hua ; Huafang Wei; Chao Liu; Yue Zhang; Siyu Liu ...
 
 
A distinct class of eukaryotic MT-A70 methyltransferases maintain symmetric DNA N6 -adenine methylation at the ApT dinucleotides as an epigenetic mark associated with transcription border= 
 
Yuanyuan Wang ; Yalan Sheng; Yongqiang Liu; Wenxin Zhang; Ting Cheng ...
 
 
Deficiency of mitoribosomal S10 protein affects translation and splicing in Arabidopsis mitochondria border= 
 
Malgorzata Kwasniak-Owczarek; Urszula Kazmierczak ; Artur Tomal; Pawel Mackiewicz; Hanna Janska
 
 
 
Nucleic Acid Enzymes
 
 
 
Loss of the ribosomal RNA methyltransferase NSUN5 impairs global protein synthesis and normal growth border= 
 
Clemens Heissenberger ; Lisa Liendl; Fabian Nagelreiter; Yulia Gonskikh; Guohuan Yang ...
 
 
Atomic structures of the RNA end-healing 5-OH kinase and 2,3-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor border= 
 
Ankan Banerjee ; Yehuda Goldgur; Beate Schwer; Stewart Shuman
 
 
A pre-catalytic non-covalent step governs DNA polymerase beta fidelity border= 
 
Khadijeh S Alnajjar ; Ivan S Krylov; Amirsoheil Negahbani; Pouya Haratipour; Boris A Kashemirov ...
 
 
 
RNA and RNA-protein complexes
 
 
 
Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy border= 
 
Alexey A Malygin ; Olesya A Krumkacheva; Dmitri M Graifer; Ivan O Timofeev; Anastasia S Ochkasova ...
 
 
The mRNA repressor TRIM71 cooperates with Nonsense-Mediated Decay factors to destabilize the mRNA of CDKN1A/p21 border= 
 
Lucia A Torres-Fernández ; Bettina Jux; Maximilian Bille; Yasmine Port; Karin Schneider ...
 
 
Single molecule analysis of effects of non-canonical guide RNAs and specificity-enhancing mutations on Cas9-induced DNA unwinding border= 
 
Ikenna C Okafor ; Digvijay Singh; Yanbo Wang; Minhee Jung; Haobo Wang ...
 
 
Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures border= 
 
Benoît Castandet ; Arnaud Germain; Amber M Hotto; David B Stern
 
 
 
Structural Biology
 
 
 
Phosphorylation orchestrates the structural ensemble of the intrinsically disordered protein HMGA1a and modulates its DNA binding to the NFkappa B promoter border= 
 
Bastian Kohl ; Xueyin Zhong; Christian Herrmann; Raphael Stoll
 
 
A DNA G-quadruplex/i-motif hybrid border=  
 
Betty Chu; Daoning Zhang; Paul J Paukstelis
 
 
Structures of 1:1 and 2:1 complexes of BMVC and MYC promoter G-quadruplex reveal a mechanism of ligand conformation adjustment for G4-recognition border= 
 
Wenting Liu ; Clement Lin; Guanhui Wu; Jixun Dai; Ta-Chau Chang ...
 
 
Crystal structure of the EcoKMcrA N-terminal domain (NEco): recognition of modified cytosine bases without flipping border= 
 
Anton Slyvka ; Evelina Zagorskait-; Honorata Czapinska; Giedrius Sasnauskas; Matthias Bochtler
 
 
 
Synthetic Biology and Bioengineering
 
 
 
Rapid in vitro production of single-stranded DNA border= 
 
Dionis Minev; Richard Guerra ; Jocelyn Y Kishi; Cory Smith; Elisha Krieg ...
 
 
Design and synthesis of pleated DNA origami nanotubes with adjustable diameters border= 
 
Jonathan F Berengut ; Julian C Berengut; Jonathan P K Doye; Domen Prešern; Akihiro Kawamoto ...
 
 
 
Corrigendum
 
 
 
Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins border= 
 
Michiel Vanmeert ; Jamoliddin Razzokov; Muhammad Usman Mirza; Stephen D Weeks; Guy Schepers ...
 
 
Robustness by intrinsically disordered C-termini and translational readthrough border= 
 
April Snofrid Kleppe ; Erich Bornberg-Bauer
 
 
 
Methods Online
 
 
 
Latent cellular analysis robustly reveals subtle diversity in large-scale single-cell RNA-seq data border= 
 
Changde Cheng ; John Easton; Celeste Rosencrance; Yan Li; Bensheng Ju ...
 
 
High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments border= 
 
Flávia S Papini ; Mona Seifert; David Dulin
 
 
Click-encoded rolling FISH for visualizing single-cell RNA polyadenylation and structures border= 
 
Feng Chen ; Min Bai; Xiaowen Cao; Yue Zhao; Jing Xue ...
 
 
Convolutional neural network model to predict causal risk factors that share complex regulatory features border= 
 
Taeyeop Lee ; Min Kyung Sung; Seulkee Lee; Woojin Yang; Jaeho Oh ...
 
 
A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment border= 
 
Ka Wai Leong ; Fangyan Yu; Viktor A Adalsteinsson; Sarah Reed; Gregory Gydush ...
 
 
Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations border= 
 
Noam Harel ; Moran Meir; Uri Gophna; Adi Stern
 
 
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