Subject: Nucleic Acids Research Table of Contents for 10 June 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 10
 
10 June 2024
 
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Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
Evaluating the oral delivery of GalNAc-conjugated siRNAs in rodents and non-human primates border= 
 
Mikyung Yu, June Qin, Xiumin Liu, Diane Ramsden, Brian Williams ...
 
 
 
Identification and in vitro characterization of UDP-GlcNAc-RNA cap-modifying and decapping enzymes border= 
 
Frederik Weber, Nikolas Alexander Motzkus, Leona Brandl, Marvin Möhler, Andrijana Alempijevic ...
 
 
 
Constraints on the emergence of RNA through non-templated primer extension with mixtures of potentially prebiotic nucleotides border= 
 
Xiwen Jia, Stephanie J Zhang, Lijun Zhou, Jack W Szostak
 
 
 
Computational Biology
 
 
 
 
Towards parsimonious generative modeling of RNA families border= 
 
Francesco Calvanese, Camille N Lambert, Philippe Nghe, Francesco Zamponi, Martin Weigt
 
 
 
BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets border= 
 
Matin Nuhamunada, Omkar S Mohite, Patrick V Phaneuf, Bernhard O Palsson, Tilmann Weber
 
 
 
 
Systematic identification of cargo-mobilizing genetic elements reveals new dimensions of eukaryotic diversity border= 
 
Emile Gluck-Thaler, Aaron A Vogan
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
Two redundant transcription factor binding sites in a single enhancer are essential for mammalian sex determination border= 
 
Meshi Ridnik, Elisheva Abberbock, Veronica Alipov, Shelly Ziv Lhermann, Shoham Kaufman ...
 
 
 
Dux activates metabolism-lactylation-MET network during early iPSC reprogramming with Brg1 as the histone lactylation reader border= 
 
Xinglin Hu, Xingwei Huang, Yue Yang, Yuchen Sun, Yanhua Zhao ...
 
 
 
FUS reads histone H3K36me3 to regulate alternative polyadenylation border=  
 
Junqi Jia, Haonan Fan, Xinyi Wan, Yuan Fang, Zhuoning Li ...
 
 
 
Molecular insights into the fine-tuning of pH-dependent ArsR-mediated regulation of the SabA adhesin in Helicobacter pylori border= 
 
Anna Åberg, Pär Gideonsson, Abhayprasad Bhat, Prachetash Ghosh, Anna Arnqvist
 
 
 
 
The zinc-finger protein Z4 cooperates with condensin II to regulate somatic chromosome pairing and 3D chromatin organization border= 
 
Marta Puerto, Mamta Shukla, Paula Bujosa, Juan Pérez-Roldán, Mònica Torràs-Llort ...
 
 
 
SIX2 promotes cell plasticity via Wnt/beta -catenin signalling in androgen receptor independent prostate cancer border= 
 
Noora Leppänen, Heidi Kaljunen, Eerika Takala, Roosa Kaarijärvi, Petri I Mäkinen ...
 
 
 
PbARID-associated chromatin remodeling events are essential for gametocyte development in Plasmodium border= 
 
Tsubasa Nishi, Izumi Kaneko, Shiroh Iwanaga, Masao Yuda
 
 
 
Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation border= 
 
Mao Chen, Bo Wu, Yuhuan Huang, Weiting Wang, Yudi Zheng ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
ARGLU1 enhances promoter-proximal pausing of RNA polymerase II and stimulates DNA damage repair border= 
 
Scott Bachus, Nikolas Akkerman, Lauren Fulham, Drayson Graves, Rafe Helwer ...
 
 
 
APLF facilitates interstrand DNA crosslink repair and replication fork protection to confer cisplatin resistance border= 
 
Cheng-Kuei Wu, Jia-Lin Shiu, Chao-Liang Wu, Chi-Feng Hung, Yen-Chih Ho ...
 
 
 
ARID1A regulates DNA repair through chromatin organization and its deficiency triggers DNA damage-mediated anti-tumor immune response border= 
 
Ali Bakr, Giuditta Della Corte, Olivera Veselinov, Simge Kelekçi, Mei-Ju May Chen ...
 
 
 
Ordered and disordered regions of the Origin Recognition Complex direct differential in vivo binding at distinct motif sequences border= 
 
Michal Chappleboim, Segev Naveh-Tassa, Miri Carmi, Yaakov Levy, Naama Barkai
 
 
 
Somatic and intergenerational G4C2 hexanucleotide repeat instability in a human C9orf72 knock-in mouse model border= 
 
Nada Kojak, Junko Kuno, Kristina E Fittipaldi, Ambereen Khan, David Wenger ...
 
 
 
Disruption of G-quadruplex dynamicity by BRCA2 abrogation instigates phase separation and break-induced replication at telomeres border= 
 
Jennifer J Lee, Hyungmin Kim, Haemin Park, UkJin Lee, Chaelim Kim ...
 
 
 
Human AAA+ ATPase FIGNL1 suppresses RAD51-mediated ultra-fine bridge formation border= 
 
Kenichiro Matsuzaki, Akira Shinohara, Miki Shinohara
 
 
 
Genomics
 
 
 
 
Precise editing of pathogenic nucleotide repeat expansions in iPSCs using paired prime editor border= 
 
Hye-Yeon Hwang, Dongmin Gim, Hwalin Yi, Hyewon Jung, Jaecheol Lee ...
 
 
 
Molecular Biology
 
 
 
 
Short 2²-O -methyl/LNA oligomers as highly-selective inhibitors of miRNA production in vitro and in vivo border= 
 
Natalia Koralewska, Eloina Corradi, Marek C Milewski, Linda Masante, Agnieszka Szczepanska ...
 
 
 
The ABCF proteins in Escherichia coli individually cope with ˜hard-to-translate' nascent peptide sequences border= 
 
Yuhei Chadani, Shun Yamanouchi, Eri Uemura, Kohei Yamasaki, Tatsuya Niwa ...
 
 
 
Fluoropyrimidines trigger decay of hypomodified tRNA in yeast border=  
 
Katharina Görlitz, Larissa Bessler, Mark Helm, Raffael Schaffrath, Roland Klassen
 
 
 
Riboswitch and small RNAs modulate btuB translation initiation in Escherichia coli and trigger distinct mRNA regulatory mechanisms border= 
 
Laurène Bastet, Alexey P Korepanov, Jonathan Jagodnik, Jonathan P Grondin, Anne-Marie Lamontagne ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
Multivalent DNAzyme agents for cleaving folded RNA border= 
 
Mikhail V Dubovichenko, Michael Batsa, Gleb A Bobkov, Gleb S Vlasov, Ahmed A El-Deeb ...
 
 
 
Functional redundancy in tRNA dihydrouridylation border=  
 
Claudia Sudol, Lea-Marie Kilz, Virginie Marchand, Quentin Thullier, Vincent Guérineau ...
 
 
 
Prokaryotic Argonaute nuclease cooperates with co-encoded RNase to acquire guide RNAs and target invader DNA border= 
 
Aleksei Agapov, Vladimir Panteleev, Ekaterina Kropocheva, Anna Kanevskaya, Daria Esyunina ...
 
 
 
The mutation R107Q alters mtSSB ssDNA compaction ability and binding dynamics border=  
 
Martial Martucci, Amandine Moretton, Aleix Tarrés-Solé, Virginie Ropars, Louise Lambert ...
 
 
 
RNA and RNA-protein complexes
 
 
 
 
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats border= 
 
Yi-Ju Tseng, Amy Krans, Indranil Malik, Xiexiong Deng, Evrim Yildirim ...
 
 
 
Implication of nucleotides near the 3² end of 16S rRNA in guarding the translational reading frame border= 
 
Alexandria Smart, Laura Lancaster, John Paul Donohue, Dustin Niblett, Harry F Noller
 
 
 
Splicing analysis of STAT3 tandem donor suggests non-canonical binding registers for U1 and U6 snRNAs border= 
 
Michal Kramárek, PÅ™emysl SouÄek, Kamila Réblová, Lucie Kajan Grodecká, TomáÅ¡ Freiberger
 
 
 
An alphacoronavirus polymerase structure reveals conserved replication factor functions border= 
 
Thomas K Anderson, Peter J Hoferle, Kennan J Chojnacki, Kenneth W Lee, Joshua J Coon ...
 
 
 
Substrate specificity of Mycobacterium tuberculosis tRNA terminal nucleotidyltransferase toxin MenT3 border= 
 
Jun Liu, Yuka Yashiro, Yuriko Sakaguchi, Tsutomu Suzuki, Kozo Tomita
 
 
 
Conserved intronic secondary structures with concealed branch sites regulate alternative splicing of poison exons border= 
 
Hao Li, Zhan Ding, Zhuo-Ya Fang, Ni Long, Hao-Yang Ang ...
 
 
 
Structural Biology
 
 
 
 
Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment border= 
 
Daniela Tarău, Felix Grünberger, Michael Pilsl, Robert Reichelt, Florian Heiß ...
 
 
 
UPF1 helicase orchestrates mutually exclusive interactions with the SMG6 endonuclease and UPF2 border= 
 
Lukas M Langer, Katharina Kurscheidt, Jérôme Basquin, Fabien Bonneau, Iuliia Iermak ...
 
 
 
Structural snapshots of phenuivirus cap-snatching and transcription border=  
 
Harry M Williams, Sigurdur R Thorkelsson, Dominik Vogel, Carola Busch, Morlin Milewski ...
 
 
 
Kinetic pathway of HIV-1 TAR cotranscriptional folding border=  
 
Lei Jin, Sicheng Zhang, Zhenwei Song, Xiao Heng, Shi-Jie Chen
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
Systematic interrogation of CRISPR antimicrobials in Klebsiella pneumoniae reveals nuclease-, guide- and strain-dependent features influencing antimicrobial activity border= 
 
Elena Vialetto, Solange Miele, Moran G Goren, Jiaqi Yu, Yanying Yu ...
 
 
 
Corrections
 
 
 
 
Correction to ˜PGS-Depot: a comprehensive resource for polygenic scores constructed by summary statistics based methods' border= 
 
 
 
 
Correction border= 
 
 
 
 
Correction to ˜Human CDK18 promotes replication stress signaling and genome stability' border= 
 
 
 
 
Correction to ˜The levels of p53 govern the hierarchy of DNA damage tolerance pathway usage' border= 
 
 
 
 
Expression of concern
 
 
 
 
Expression of Concern on ˜MCPIP1 ribonuclease exhibits broad-spectrum antiviral effects through viral RNA binding and degradation' border= 
 
 
 
 
Methods
 
 
 
 
Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries border= 
 
Weiyi Li, Darach Miller, Xianan Liu, Lorenzo Tosi, Lamia Chkaiban ...
 
 
 
Massively parallel dissection of RNA in RNA'protein interactions in vivo border=  
 
Yu Hsuan Lee, Evan P Hass, Will Campodonico, Yong Kyu Lee, Erika Lasda ...
 
 
 
A bisulfite-assisted and ligation-based qPCR amplification technology for locus-specific pseudouridine detection at base resolution border= 
 
Xin Fang, Ruiqi Zhao, Yafen Wang, Mei Sun, Jin Xu ...
 
 
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