Subject: Nucleic Acids Research Table of Contents for 24 January 2020 ------=_Part_1292423126.1579024392618 Content-Type: text/plain;charset=UTF-8 Oxford Academic *** Nucleic Acids Research *** Volume 48, Issue 2, 24 January 2020 Read this issue (https://academic.oup.com/nar/issue/48/2) ------------------------------ 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. ------------------------------ ============================= NAR Breakthrough Article ============================Structural basis of non-canonical transcriptional regulation by the σA-bound iron-sulfur protein WhiB1 in M. tuberculosis Tao Wan, Shanren Li, Daisy Guiza Beltran, Andrew Schacht, Lu Zhang (https://academic.oup.com/nar/article/48/2/501/5661089) ============================= Chemical Biology and Nucleic Acid Chemistry ============================Inhibition of histone deacetylase 1 (HDAC1) and HDAC2 enhances CRISPR/Cas9 genome editing Bin Liu, Siwei Chen, Anouk La Rose, Deng Chen, Fangyuan Cao (https://academic.oup.com/nar/article/48/2/517/5651331) ============================= Computational Biology ============================Allele-specific single-cell RNA sequencing reveals different architectures of intrinsic and extrinsic gene expression noises Mengyi Sun, Jianzhi Zhang (https://academic.oup.com/nar/article/48/2/533/5651327) Free energy landscape of salt-actuated reconfigurable DNA nanodevices Ze Shi, Gaurav Arya (https://academic.oup.com/nar/article/48/2/548/5651318) Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes Justin A Lemkul (https://academic.oup.com/nar/article/48/2/561/5661083) ============================= Data Resources and Analyses ============================RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools Marcin Magnus, Maciej Antczak, Tomasz Zok, Jakub Wiedemann, Piotr Lukasiak (https://academic.oup.com/nar/article/48/2/576/5651330) Specific enhancer selection by IRF3, IRF5 and IRF9 is determined by ISRE half-sites, 5' and 3' flanking bases, collaborating transcription factors and the chromatin environment in a combinatorial fashion Mária Csumita, Attila Csermely, Attila Horvath, Gergely Nagy, Fanny Monori (https://academic.oup.com/nar/article/48/2/589/5651321) mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations Annie Yim, Prasanna Koti, Adrien Bonnard, Fabio Marchiano, Milena Dürrbaum (https://academic.oup.com/nar/article/48/2/605/5651332) ============================= Gene Regulation, Chromatin and Epigenetics ============================Sam68 binds Alu-rich introns in SMN and promotes pre-mRNA circularization Vittoria Pagliarini, Ariane Jolly, Pamela Bielli, Valentina Di Rosa, Pierre De la Grange (https://academic.oup.com/nar/article/48/2/633/5645010) Different class IIa HDACs repressive complexes regulate specific epigenetic responses related to cell survival in leiomyosarcoma cells Eros Di Giorgio, Emiliano Dalla, Elisa Franforte, Harikrishnareddy Paluvai, Martina Minisini (https://academic.oup.com/nar/article/48/2/646/5637592) SIRT1/2 orchestrate acquisition of DNA methylation and loss of histone H3 activating marks to prevent premature activation of inflammatory genes in macrophages Tianlu Li, Antonio Garcia-Gomez, Octavio Morante-Palacios, Laura Ciudad, Sevgi zkaramehmet (https://academic.oup.com/nar/article/48/2/665/5651320) Heterochromatin protein 1alpha interacts with parallel RNA and DNA G-quadruplexes Ruby J Roach, Miguel Garavís, Carlos González, Geoffrey B Jameson, Vyacheslav V Filichev (https://academic.oup.com/nar/article/48/2/682/5651329) ============================= Genome Integrity, Repair and Replication ============================DSS1 interacts with and stimulates RAD52 to promote the repair of DSBs Barbora Stefanovie, Sarah R Hengel, Jarmila Mlcouskova, Jana Prochazkova, Mario Spirek (https://academic.oup.com/nar/article/48/2/694/5651317) Identification of a novel structure-specific endonuclease AziN that contributes to the repair of azinomycin B-mediated DNA interstrand crosslinks Xiaorong Chen, Yuedi Sun, Shan Wang, Kun Ying, Le Xiao (https://academic.oup.com/nar/article/48/2/709/5622706) DNA barcoding reveals that injected transgenes are predominantly processed by homologous recombination in mouse zygote Alexander Smirnov, Veniamin Fishman, Anastasia Yunusova, Alexey Korablev, Irina Serova (https://academic.oup.com/nar/article/48/2/719/5628924) USP14 is a deubiquitinase for Ku70 and critical determinant of non-homologous end joining repair in autophagy and PTEN-deficient cells Arishya Sharma, Turkeya Alswillah, Isha Kapoor, Pal Debjani, Belinda Willard (https://academic.oup.com/nar/article/48/2/736/5628926) ============================= Genomics ============================Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements Aude Bernheim, David Bikard, Marie Touchon, Eduardo P C Rocha (https://academic.oup.com/nar/article/48/2/748/5634034) Point mutations in topoisomerase I alter the mutation spectrum in E. coli and impact the emergence of drug resistance genotypes Amit Bachar, Elad Itzhaki, Shmuel Gleizer, Melina Shamshoom, Ron Milo (https://academic.oup.com/nar/article/48/2/761/5645004) ============================= Molecular Biology ============================Ribosomal protein gene RPL9 variants can differentially impair ribosome function and cellular metabolism Marco Lezzerini, Marianna Penzo, Marie-Françoise O'Donohue, Carolina Marques dos Santos Vieira, Manon Saby (https://academic.oup.com/nar/article/48/2/770/5651335) Structural basis for the dimerization of Gemin5 and its role in protein recruitment and translation control María Moreno-Morcillo, Rosario Francisco-Velilla, Azman Embarc-Buh, Javier Fernández-Chamorro, Santiago Ramón-Maiques (https://academic.oup.com/nar/article/48/2/788/5651328) Hybridization-mediated off-target effects of splice-switching antisense oligonucleotides Juergen Scharner, Wai Kit Ma, Qian Zhang, Kuan-Ting Lin, Frank Rigo (https://academic.oup.com/nar/article/48/2/802/5658446) ============================= Nucleic Acid Enzymes ============================Oxidative damage diminishes mitochondrial DNA polymerase replication fidelity Andrew P Anderson, Xuemei Luo, William Russell, Y Whitney Yin (https://academic.oup.com/nar/article/48/2/817/5651319) The human methyltransferase ZCCHC4 catalyses N6-methyladenosine modification of 28S ribosomal RNA Rita Pinto, Cathrine B Vågbø, Magnus E Jakobsson, Yeji Kim, Marijke P Baltissen (https://academic.oup.com/nar/article/48/2/830/5651334) Cross-subunit catalysis and a new phenomenon of recessive resurrection in Escherichia coli RNase E Nida Ali, Jayaraman Gowrishankar (https://academic.oup.com/nar/article/48/2/847/5658448) ============================= RNA and RNA-protein complexes ============================The FMRP--MOV10 complex: a translational regulatory switch modulated by G-Quadruplexes Phillip J Kenny, Miri Kim, Geena Skariah, Joshua Nielsen, Monica C Lannom (https://academic.oup.com/nar/article/48/2/862/5628922) Characterization of zygotic genome activation-dependent maternal mRNA clearance in mouse Qian-Qian Sha, Ye-Zhang Zhu, Sen Li, Yu Jiang, Lu Chen (https://academic.oup.com/nar/article/48/2/879/5644991) Negative cooperativity between Gemin2 and RNA provides insights into RNA selection and the SMN complex's release in snRNP assembly Hongfei Yi, Li Mu, Congcong Shen, Xi Kong, Yingzhi Wang (https://academic.oup.com/nar/article/48/2/895/5651324) mRNA regions where 80S ribosomes pause during translation elongation in vivo interact with protein uS19, a component of the decoding site Elena S Babaylova, Alexander V Gopanenko, Konstantin N Bulygin, Alexey E Tupikin, Marsel R Kabilov (https://academic.oup.com/nar/article/48/2/912/5658444) ============================= Structural Biology ============================High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label Marcel Heinz, Nicole Erlenbach, Lukas S Stelzl, Grace Thierolf, Nilesh R Kamble (https://academic.oup.com/nar/article/48/2/924/5644995) Mechanism of conditional partner selectivity in MITF/TFE family transcription factors with a conserved coiled coil stammer motif Vivian Pogenberg, Josué Ballesteros- lvarez, Romana Schober, Ingibjörg Sigvaldadóttir, Agnieszka Obarska-Kosinska (https://academic.oup.com/nar/article/48/2/934/5644993) Structure of an RNA aptamer in complex with the fluorophore tetramethylrhodamine Elke Duchardt-Ferner, Michael Juen, Benjamin Bourgeois, Tobias Madl, Christoph Kreutz (https://academic.oup.com/nar/article/48/2/949/5637584) Conformation-dependent restraints for polynucleotides: the sugar moiety Marcin Kowiel, Dariusz Brzezinski, Miroslaw Gilski, Mariusz Jaskolski (https://academic.oup.com/nar/article/48/2/962/5651323) ============================= Synthetic Biology and Bioengineering ============================Expanding the editable genome and CRISPR--Cas9 versatility using DNA cutting-free gene targeting based on in trans paired nicking Xiaoyu Chen, Francesca Tasca, Qian Wang, Jin Liu, Josephine M Janssen (https://academic.oup.com/nar/article/48/2/974/5651333) Design of a programmable biosensor-CRISPRi genetic circuits for dynamic and autonomous dual-control of metabolic flux in Bacillus subtilis Yaokang Wu, Taichi Chen, Yanfeng Liu, Rongzhen Tian, Xueqin Lv (https://academic.oup.com/nar/article/48/2/996/5651338) ============================= Corrigendum ============================Targeted insertional mutagenesis libraries for deep domain insertion profiling Willow Coyote-Maestas, David Nedrud, Steffan Okorafor, Yungui He, Daniel Schmidt (https://academic.oup.com/nar/article/48/2/1010/5651339) ============================= Methods Online ============================RiboVIEW: a computational framework for visualization, quality control and statistical analysis of ribosome profiling data Carine Legrand, Francesca Tuorto (https://academic.oup.com/nar/article/48/2/e7/5645003) HaloTag-based conjugation of proteins to barcoding-oligonucleotides Junshi Yazaki, Yusuke Kawashima, Taisaku Ogawa, Atsuo Kobayashi, Mayu Okoshi (https://academic.oup.com/nar/article/48/2/e8/5634036) Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination Joshua L Wetzel, Mona Singh (https://academic.oup.com/nar/article/48/2/e9/5645009) TFregulomeR reveals transcription factors' context-specific features and functions Quy Xiao Xuan Lin, Denis Thieffry, Sudhakar Jha, Touati Benoukraf (https://academic.oup.com/nar/article/48/2/e10/5637590) Targeted insertional mutagenesis libraries for deep domain insertion profiling Willow Coyote-Maestas, David Nedrud, Steffan Okorafor, Yungui He, Daniel Schmidt (https://academic.oup.com/nar/article/48/2/e11/5634037) Mapping RNA--capsid interactions and RNA secondary structure within virus particles using next-generation sequencing Yiyang Zhou, Andrew Routh (https://academic.oup.com/nar/article/48/2/e12/5651326) 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.biology.mcmaster.ca. ------=_Part_1292423126.1579024392618 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 2
 
24 January 2020
 
button-issue.png
 
 
NAR Breakthrough Article
 
 
 
Structural basis of non-canonical transcriptional regulation by the σA-bound iron-sulfur protein WhiB1 in M. tuberculosis  border= 
 
Tao Wan; Shanren Li ; Daisy Guiza Beltran; Andrew Schacht; Lu Zhang ...
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
Inhibition of histone deacetylase 1 (HDAC1) and HDAC2 enhances CRISPR/Cas9 genome editing border= 
 
Bin Liu ; Siwei Chen; Anouk La Rose; Deng Chen; Fangyuan Cao ...
 
 
 
Computational Biology
 
 
 
Allele-specific single-cell RNA sequencing reveals different architectures of intrinsic and extrinsic gene expression noises border= 
 
Mengyi Sun ; Jianzhi Zhang
 
 
Free energy landscape of salt-actuated reconfigurable DNA nanodevices border= 
 
Ze Shi; Gaurav Arya
 
 
Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes border= 
 
Justin A Lemkul
 
 
 
Data Resources and Analyses
 
 
 
RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools border= 
 
Marcin Magnus ; Maciej Antczak; Tomasz Zok; Jakub Wiedemann; Piotr Lukasiak ...
 
 
Specific enhancer selection by IRF3, IRF5 and IRF9 is determined by ISRE half-sites, 5 and 3 flanking bases, collaborating transcription factors and the chromatin environment in a combinatorial fashion border= 
 
Mária Csumita ; Attila Csermely; Attila Horvath; Gergely Nagy; Fanny Monori ...
 
 
mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations border= 
 
Annie Yim ; Prasanna Koti; Adrien Bonnard; Fabio Marchiano; Milena Dürrbaum ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
Sam68 binds Alu-rich introns in SMN and promotes pre-mRNA circularization border= 
 
Vittoria Pagliarini; Ariane Jolly ; Pamela Bielli; Valentina Di Rosa; Pierre De la Grange ...
 
 
Different class IIa HDACs repressive complexes regulate specific epigenetic responses related to cell survival in leiomyosarcoma cells border= 
 
Eros Di Giorgio ; Emiliano Dalla; Elisa Franforte; Harikrishnareddy Paluvai; Martina Minisini ...
 
 
SIRT1/2 orchestrate acquisition of DNA methylation and loss of histone H3 activating marks to prevent premature activation of inflammatory genes in macrophages border= 
 
Tianlu Li ; Antonio Garcia-Gomez; Octavio Morante-Palacios; Laura Ciudad; Sevgi Özkaramehmet ...
 
 
Heterochromatin protein 1alpha interacts with parallel RNA and DNA G-quadruplexes border= 
 
Ruby J Roach ; Miguel Garavís; Carlos González; Geoffrey B Jameson; Vyacheslav V Filichev ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
DSS1 interacts with and stimulates RAD52 to promote the repair of DSBs border= 
 
Barbora Stefanovie ; Sarah R Hengel; Jarmila Mlcouskova; Jana Prochazkova; Mario Spirek ...
 
 
Identification of a novel structure-specific endonuclease AziN that contributes to the repair of azinomycin B-mediated DNA interstrand crosslinks border= 
 
Xiaorong Chen ; Yuedi Sun; Shan Wang; Kun Ying; Le Xiao ...
 
 
DNA barcoding reveals that injected transgenes are predominantly processed by homologous recombination in mouse zygote border= 
 
Alexander Smirnov ; Veniamin Fishman; Anastasia Yunusova; Alexey Korablev; Irina Serova ...
 
 
USP14 is a deubiquitinase for Ku70 and critical determinant of non-homologous end joining repair in autophagy and PTEN-deficient cells border= 
 
Arishya Sharma ; Turkeya Alswillah; Isha Kapoor; Pal Debjani; Belinda Willard ...
 
 
 
Genomics
 
 
 
Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements border= 
 
Aude Bernheim; David Bikard; Marie Touchon; Eduardo P C Rocha
 
 
Point mutations in topoisomerase I alter the mutation spectrum in E. coli and impact the emergence of drug resistance genotypes border= 
 
Amit Bachar; Elad Itzhaki; Shmuel Gleizer; Melina Shamshoom; Ron Milo ...
 
 
 
Molecular Biology
 
 
 
Ribosomal protein gene RPL9 variants can differentially impair ribosome function and cellular metabolism border= 
 
Marco Lezzerini ; Marianna Penzo; Marie-Françoise O'Donohue; Carolina Marques dos Santos Vieira; Manon Saby ...
 
 
Structural basis for the dimerization of Gemin5 and its role in protein recruitment and translation control border= 
 
María Moreno-Morcillo ; Rosario Francisco-Velilla; Azman Embarc-Buh; Javier Fernández-Chamorro; Santiago Ramón-Maiques ...
 
 
Hybridization-mediated off-target effects of splice-switching antisense oligonucleotides border= 
 
Juergen Scharner ; Wai Kit Ma; Qian Zhang; Kuan-Ting Lin; Frank Rigo ...
 
 
 
Nucleic Acid Enzymes
 
 
 
Oxidative damage diminishes mitochondrial DNA polymerase replication fidelity border= 
 
Andrew P Anderson ; Xuemei Luo; William Russell; Y Whitney Yin
 
 
The human methyltransferase ZCCHC4 catalyses N6 -methyladenosine modification of 28S ribosomal RNA border= 
 
Rita Pinto; Cathrine B Vågbø; Magnus E Jakobsson; Yeji Kim; Marijke P Baltissen ...
 
 
Cross-subunit catalysis and a new phenomenon of recessive resurrection in Escherichia coli RNase E border= 
 
Nida Ali; Jayaraman Gowrishankar
 
 
 
RNA and RNA-protein complexes
 
 
 
The FMRP'MOV10 complex: a translational regulatory switch modulated by G-Quadruplexes border= 
 
Phillip J Kenny ; Miri Kim; Geena Skariah; Joshua Nielsen; Monica C Lannom ...
 
 
Characterization of zygotic genome activation-dependent maternal mRNA clearance in mouse border= 
 
Qian-Qian Sha ; Ye-Zhang Zhu; Sen Li; Yu Jiang; Lu Chen ...
 
 
Negative cooperativity between Gemin2 and RNA provides insights into RNA selection and the SMN complex's release in snRNP assembly border= 
 
Hongfei Yi ; Li Mu; Congcong Shen; Xi Kong; Yingzhi Wang ...
 
 
mRNA regions where 80S ribosomes pause during translation elongation in vivo interact with protein uS19, a component of the decoding site border= 
 
Elena S Babaylova ; Alexander V Gopanenko; Konstantin N Bulygin; Alexey E Tupikin; Marsel R Kabilov ...
 
 
 
Structural Biology
 
 
 
High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label border= 
 
Marcel Heinz ; Nicole Erlenbach; Lukas S Stelzl; Grace Thierolf; Nilesh R Kamble ...
 
 
Mechanism of conditional partner selectivity in MITF/TFE family transcription factors with a conserved coiled coil stammer motif border= 
 
Vivian Pogenberg ; Josué Ballesteros-Álvarez; Romana Schober; Ingibjörg Sigvaldadóttir; Agnieszka Obarska-Kosinska ...
 
 
Structure of an RNA aptamer in complex with the fluorophore tetramethylrhodamine border= 
 
Elke Duchardt-Ferner ; Michael Juen; Benjamin Bourgeois; Tobias Madl; Christoph Kreutz ...
 
 
Conformation-dependent restraints for polynucleotides: the sugar moiety border= 
 
Marcin Kowiel ; Dariusz Brzezinski; Miroslaw Gilski; Mariusz Jaskolski
 
 
 
Synthetic Biology and Bioengineering
 
 
 
Expanding the editable genome and CRISPR'Cas9 versatility using DNA cutting-free gene targeting based on in trans paired nicking border= 
 
Xiaoyu Chen; Francesca Tasca ; Qian Wang; Jin Liu; Josephine M Janssen ...
 
 
Design of a programmable biosensor-CRISPRi genetic circuits for dynamic and autonomous dual-control of metabolic flux in Bacillus subtilis  border= 
 
Yaokang Wu; Taichi Chen ; Yanfeng Liu; Rongzhen Tian; Xueqin Lv ...
 
 
 
Corrigendum
 
 
 
Targeted insertional mutagenesis libraries for deep domain insertion profiling border= 
 
Willow Coyote-Maestas ; David Nedrud; Steffan Okorafor; Yungui He; Daniel Schmidt
 
 
 
Methods Online
 
 
 
RiboVIEW: a computational framework for visualization, quality control and statistical analysis of ribosome profiling data border= 
 
Carine Legrand ; Francesca Tuorto
 
 
HaloTag-based conjugation of proteins to barcoding-oligonucleotides border= 
 
Junshi Yazaki ; Yusuke Kawashima; Taisaku Ogawa; Atsuo Kobayashi; Mayu Okoshi ...
 
 
Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination border= 
 
Joshua L Wetzel ; Mona Singh
 
 
TFregulomeR reveals transcription factors' context-specific features and functions border= 
 
Quy Xiao Xuan Lin ; Denis Thieffry; Sudhakar Jha; Touati Benoukraf
 
 
Targeted insertional mutagenesis libraries for deep domain insertion profiling border= 
 
Willow Coyote-Maestas ; David Nedrud; Steffan Okorafor; Yungui He; Daniel Schmidt
 
 
Mapping RNA'capsid interactions and RNA secondary structure within virus particles using next-generation sequencing border= 
 
Yiyang Zhou ; Andrew Routh
 
 
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