Subject: Nucleic Acids Research Table of Contents for 12 April 2024 Oxford Academic
 
 
 
Oxford Academic
 
 
 
 
New issue alert
 
 
 
 
Celebrating 50 years of NAR
 

Nucleic Acids Research is celebrating its 50th anniversary this year. We owe our success to the incredible work of the three founding editors, Richard T. Walker and A. Stanley Jones at the University of Birmingham in the UK, and Dieter Söll at Yale University in the USA. Their vision and dedication have been carried forward by the editors who followed them, as well as our authors and reviewers. Today, NAR remains one of the leading journals in the biological sciences. 

Celebrate our 50th anniversary with us
 
 
 
 
Nucleic Acids Research  
Volume 52 Issue 6
 
12 April 2024
 
button-issue.png
 
 
NAR Breakthrough Article
 
 
 
 
CRISPR antiphage defence mediated by the cyclic nucleotide-binding membrane protein Csx23 border= 
 
Sabine Grüschow, Stuart McQuarrie, Katrin Ackermann, Stephen McMahon, Bela E Bode ...
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
Programmable RNA 5-methylcytosine (m5 C) modification of cellular RNAs by dCasRx conjugated methyltransferase and demethylase border= 
 
Tao Zhang, Feiyu Zhao, Jinze Li, Xiaodi Sun, Xiyun Zhang ...
 
 
 
Chemical modification patterns for microRNA therapeutic mimics: a structure-activity relationship (SAR) case-study on miR-200c border= 
 
Marion Garreau, Julie Weidner, Russell Hamilton, Ewa Kolosionek, Naoko Toki ...
 
 
 
Bioorthogonal labeling and profiling of N6-isopentenyladenosine (i6 A) modified RNA border= 
 
Yuanyuan Li, Hongling Zhou, Shasha Chen, Yinan Li, Yuyang Guo ...
 
 
 
Computational Biology
 
 
 
 
Functional identification of cis -regulatory long noncoding RNAs at controlled false discovery rates border= 
 
Bhavya Dhaka, Marc Zimmerli, Daniel Hanhart, Mario B Moser, Hugo Guillen-Ramirez ...
 
 
 
 
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline border= 
 
Jérôme Rihon, Charles-Alexandre Mattelaer, Rinaldo Wander Montalvão, Mathy Froeyen, Vitor Bernardes Pinheiro ...
 
 
 
Data Resources and Analyses
 
 
 
 
Comprehensive map of ribosomal 2²-O-methylation and C/D box snoRNAs in Drosophila melanogaster border= 
 
Athena Sklias, Sonia Cruciani, Virginie Marchand, Mariangela Spagnuolo, Guillaume Lavergne ...
 
 
 
Comprehensive transcriptome analysis reveals altered mRNA splicing and post-transcriptional changes in the aged mouse brain border= 
 
Nisha Hemandhar Kumar, Verena Kluever, Emanuel Barth, Sebastian Krautwurst, Mattia Furlan ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
Acetylation of xenogeneic silencer H-NS regulates biofilm development through the nitrogen homeostasis regulator in Shewanella border= 
 
Xiaoxiao Liu, Jun Li, Zhixuan Zhang, Yizhou He, Mingfang Wang ...
 
 
 
Genetic variation is a key determinant of chromatin accessibility and drives differences in the regulatory landscape of C57BL/6J and 129S1/SvImJ mice border= 
 
Juho Mononen, Mari Taipale, Marjo Malinen, Bharadwaja Velidendla, Einari Niskanen ...
 
 
 
 
Nitric oxide sensor NsrR is the key direct regulator of magnetosome formation and nitrogen metabolism in Magnetospirillum border= 
 
Bo Pang, Haolan Zheng, Shijia Ma, Jiesheng Tian, Ying Wen
 
 
 
Lethal perturbation of an Escherichia coli regulatory network is triggered by a restriction-modification system's regulator and can be mitigated by excision of the cryptic prophage Rac border= 
 
Katarzyna Gucwa, Ewa Wons, Aleksandra Wisniewska, Marcin Jakalski, Zuzanna Dubiak ...
 
 
 
Identification of promoter activity in gene-less cassettes from Vibrionaceae superintegrons border= 
 
Paula Blanco, Alberto Hipólito, Lucía García-Pastor, Filipa Trigo da Roza, Laura Toribio-Celestino ...
 
 
 
NELF focuses sites of initiation and maintains promoter architecture border=  
 
Juan F Santana, Benjamin M Spector, Gustavo A Suarez, Donal S Luse, David H Price
 
 
 
Chromatin remodeler CHD8 is required for spermatogonial proliferation and early meiotic progression border= 
 
Kenta Nitahara, Atsuki Kawamura, Yuka Kitamura, Kiyoko Kato, Satoshi H Namekawa ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
The dimeric deubiquitinase USP28 integrates 53BP1 and MYC functions to limit DNA damage border= 
 
Chao Jin, Elias Einig, Wenshan Xu, Ravi Babu Kollampally, Andreas Schlosser ...
 
 
 
H2A.Z is involved in premature aging and DSB repair initiation in muscle fibers border= 
 
Edwige Belotti, Nicolas Lacoste, Arslan Iftikhar, Thomas Simonet, Christophe Papin ...
 
 
 
Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts border= 
 
Barbara Trifault, Victoria Mamontova, Giacomo Cossa, Sabina Ganskih, Yuanjie Wei ...
 
 
 
DNA hypomethylation activates Cdk4/6 and Atr to induce DNA replication and cell cycle arrest to constrain liver outgrowth in zebrafish border= 
 
Bhavani P Madakashira, Elena Magnani, Shashi Ranjan, Kirsten C Sadler
 
 
 
Linear DNA-driven recombination in mammalian mitochondria border=  
 
Georgios Fragkoulis, Anu Hangas, Zsófia Fekete, Craig Michell, Carlos T Moraes ...
 
 
 
Genomics
 
 
 
 
The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis border= 
 
Qiushi Xu, Yunlong Zhang, Wei Xu, Dong Liu, Wenfei Jin ...
 
 
 
Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity border= 
 
Bart Edelbroek, Jonas Kjellin, Inna Biryukova, Zhen Liao, Torgny Lundberg ...
 
 
 
Molecular Biology
 
 
 
 
Cross-contamination of CRISPR guides and other unrelated nucleotide sequences among commercial oligonucleotides border= 
 
Hiroshi Arakawa, Hiromi Miura, Rolen M Quadros, Masato Ohtsuka, Channabasavaiah B Gurumurthy
 
 
 
Resection of DNA double-strand breaks activates Mre11'Rad50'Nbs1- and Rad9'Hus1'Rad1-dependent mechanisms that redundantly promote ATR checkpoint activation and end processing in Xenopus egg extracts border= 
 
Kensuke Tatsukawa, Reihi Sakamoto, Yoshitaka Kawasoe, Yumiko Kubota, Toshiki Tsurimoto ...
 
 
 
A sensitive and scalable fluorescence anisotropy single stranded RNA targeting approach for monitoring riboswitch conformational states border= 
 
Maira Rivera, Omma S Ayon, Suzana Diaconescu-Grabari, Joshua Pottel, Nicolas Moitessier ...
 
 
 
Novel mechanisms of diversity generation in Acinetobacter baumannii resistance islands driven by Tn7-like elements border= 
 
Alberto Correa, III, Saadlee Shehreen, Laura Chacon Machado, Jordan Thesier, Lille M Cunic ...
 
 
 
Cryptic proteins translated from deletion-containing viral genomes dramatically expand the influenza virus proteome border= 
 
Jordan N Ranum, Mitchell P Ledwith, Fadi G Alnaji, Meghan Diefenbacher, Richard Orton ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
Multifaceted roles of t6 A biogenesis in efficiency and fidelity of mitochondrial gene expression border= 
 
Yong Zhang, Jing-Bo Zhou, Yue Yin, En-Duo Wang, Xiao-Long Zhou
 
 
 
Innate programmable DNA binding by CRISPR-Cas12m effectors enable efficient base editing border= 
 
Greta Bigelyte, Brigita Duchovska, Rimante Zedaveinyte, Giedrius Sasnauskas, Tomas Sinkunas ...
 
 
 
Single-molecule characterization of Sen1 translocation properties provides insights into eukaryotic factor-dependent transcription termination border= 
 
Shuang Wang, Zhong Han, Terence R Strick
 
 
 
Identification of Hammerhead-variant ribozyme sequences in SARS-CoV-2 border=  
 
Getong Liu, Hengyi Jiang, Dongrong Chen, Alastair I H Murchie
 
 
 
A jingmenvirus RNA-dependent RNA polymerase structurally resembles the flavivirus counterpart but with different features at the initiation phase border= 
 
Xinyu Wang, Xuping Jing, Junming Shi, Qiaojie Liu, Shu Shen ...
 
 
 
RNA and RNA-protein complexes
 
 
 
 
THUMPD2 catalyzes the N2 -methylation of U6 snRNA of the spliceosome catalytic center and regulates pre-mRNA splicing and retinal degeneration border= 
 
Wen-Qing Yang, Jian-Yang Ge, Xiaofeng Zhang, Wen-Yu Zhu, Lin Lin ...
 
 
 
Dissolution of ribonucleoprotein condensates by the embryonic stem cell protein L1TD1 border= 
 
Sang Woo Jin, Youngmo Seong, Dayoung Yoon, Young-Soo Kwon, Hoseok Song
 
 
 
LINE-1 mRNA 3² end dynamics shape its biology and retrotransposition potential border= 
 
Damian M Janecki, Raneet Sen, Natalia Szóstak, Arkadiusz Kajdasz, Martyna KordyÅ› ...
 
 
 
NAC and Zuotin/Hsp70 chaperone systems coexist at the ribosome tunnel exit in vivo border= 
 
Thomas Ziegelhoffer, Amit K Verma, Wojciech Delewski, Brenda A Schilke, Paige M Hill ...
 
 
 
Influence of RNA circularity on Target RNA-Directed MicroRNA Degradation border=  
 
Federico Fuchs Wightman, Jerónimo Lukin, Sebastián A Giusti, Michael Soutschek, Laureano Bragado ...
 
 
 
Structural Biology
 
 
 
 
Site-specific incorporation of a fluorescent nucleobase analog enhances i-motif stability and allows monitoring of i-motif folding inside cells border= 
 
Bartomeu Mir, Israel Serrano-Chacón, Pedro Medina, Veronica Macaluso, Montserrat Terrazas ...
 
 
 
Structure of native four-repeat satellite III sequence with non-canonical base interactions border= 
 
Erin Chen, Marko Trajkovski, Hyun Kyung Lee, Samantha Nyovanie, Kailey N Martin ...
 
 
 
Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition border= 
 
Ben-Ge Xin, Ling-Yun Huang, Ling-Gang Yuan, Na-Nv Liu, Hai-Hong Li ...
 
 
 
Conserved structures and dynamics in 5²-proximal regions of Betacoronavirus RNA genomes border= 
 
Tales Rocha de Moura, Elżbieta Purta, Agata Bernat, Eva M Martín-Cuevas, MaÅ‚gorzata Kurkowska ...
 
 
 
Molecular mechanism of the one-component regulator RccR on bacterial metabolism and virulence border= 
 
Yibo Zhu, Xingyu Mou, Yingjie Song, Qianqian Zhang, Bo Sun ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
An engineered baculoviral protein and DNA co-delivery system for CRISPR-based mammalian genome editing border= 
 
Julien Capin, Alexandra Harrison, Renata A Raele, Sathish K N Yadav, Dominique Baiwir ...
 
 
 
Peptide nucleic acid-assisted generation of targeted double-stranded DNA breaks with T7 endonuclease I border= 
 
Rashid Aman, Muntjeeb M Syed, Ahmed Saleh, Firdaws Melliti, Sivakrishna Rao Gundra ...
 
 
 
Correction
 
 
 
 
Correction to ˜Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9' 
 
 
 
 
Correction to ˜Genomes OnLine Database (GOLD) v.8: overview and updates' border= 
 
 
 
 
Correction to ˜Functional identification of cis-regulatory long noncoding RNAs at controlled false discovery rates' border= 
 
 
 
 
Correction to ˜PathBank 2.0'the pathway database for model organism metabolomics' border= 
 
 
 
 
Correction to ˜Cell cycle regulated DNA methyltransferase: fluorescent tracking of a DNA strand-separation mechanism and identification of the responsible protein motif' border= 
 
 
 
 
Correction to ˜A dual-activity topoisomerase complex promotes both transcriptional activation and repression in response to starvation' 
 
 
 
 
Methods
 
 
 
 
Global identification of mRNA-interacting circular RNAs by CLiPPR-Seq border= 
 
Suman Singh, Sharmishtha Shyamal, Arundhati Das, Amaresh C Panda
 
 
 
CRISPR-COPIES: an in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration border= 
 
Aashutosh Girish Boob, Zhixin Zhu, Pattarawan Intasian, Manan Jain, Vassily Andrew Petrov ...
 
 
 
Prediction of protein-RNA interactions from single-cell transcriptomic data border=  
 
Jonathan Fiorentino, Alexandros Armaos, Alessio Colantoni, Gian Gaetano Tartaglia
 
 
 
BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies border= 
 
Wanding Zhou, Benjamin K Johnson, Jacob Morrison, Ian Beddows, James Eapen ...
 
 
 
Employing bimodal representations to predict DNA bendability within a self-supervised pre-trained framework border= 
 
Minghao Yang, Shichen Zhang, Zhihang Zheng, Pengfei Zhang, Yan Liang ...
 
 
 
A system of reporters for comparative investigation of EJC-independent and EJC-enhanced nonsense-mediated mRNA decay border= 
 
Divya Kolakada, Amy E Campbell, Laura Baquero Galvis, Zhongyou Li, Mlana Lore ...
 
 
Unsubscribe       Manage 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 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.