Subject: Nucleic Acids Research Table of Contents for 8 July 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 12
 
8 July 2024
 
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Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
Site-specific regulation of RNA editing with ribose-modified nucleoside analogs in ADAR guide strands border= 
 
Victorio Jauregui-Matos, Olivia Jacobs, Randall Ouye, Sukanya Mozumder, Prince J Salvador ...
 
 
 
Unlocking the potential of protein-derived peptides to target G-quadruplex DNA: from recognition to anticancer activity border= 
 
Francesco Merlino, Simona Marzano, Pasquale Zizza, Federica D'Aria, Nicola Grasso ...
 
 
 
Computational Biology
 
 
 
 
Skipping events impose repeated binding attempts: profound kinetic implications of protein'DNA conformational changes border= 
 
Elena Rogoulenko, Yaakov Levy
 
 
 
Generating, modeling and evaluating a large-scale set of CRISPR/Cas9 off-target sites with bulges border= 
 
Ofir Yaish, Yaron Orenstein
 
 
 
CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes border= 
 
David Farré-Gil, Juan Pablo Arcon, Charles A Laughton, Modesto Orozco
 
 
 
 
In silico design of DNA sequences for in vivo nucleosome positioning border= 
 
Etienne Routhier, Alexandra Joubert, Alex Westbrook, Edgard Pierre, Astrid Lancrey ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
CARM1 hypermethylates the NuRD chromatin remodeling complex to promote cell cycle gene expression and breast cancer development border= 
 
Xue Chen, Ming-feng Huang, Da-meng Fan, Yao-hui He, Wen-juan Zhang ...
 
 
 
A-MYB substitutes for B-MYB in activating cell cycle genes and in stimulating proliferation border= 
 
Robin Kohler, Kurt Engeland
 
 
 
Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters border= 
 
Emily Hsu, Katherine Hutchison, Yao Liu, Charles M Nicolet, Shannon Schreiner ...
 
 
 
Protein phosphatase PP1 regulation of RNA polymerase II transcription termination and allelic exclusion of VSG genes in trypanosomes border= 
 
Rudo Kieft, Yang Zhang, Haidong Yan, Robert J Schmitz, Robert Sabatini
 
 
 
 
New Drosophila promoter-associated architectural protein Mzfp1 interacts with CP190 and is required for housekeeping gene expression and insulator activity border= 
 
Vladimir Sokolov, Olga Kyrchanova, Natalia Klimenko, Anna Fedotova, Airat Ibragimov ...
 
 
 
NF-kappa B factors cooperate with Su(Hw)/E4F1 to balance Drosophila/human immune responses via modulating dynamic expression of miR-210  border= 
 
Hongjian Zhou, Yu Huang, Chaolong Jia, Yujia Pang, Li Liu ...
 
 
 
Alternative translation initiation by ribosomal leaky scanning produces multiple isoforms of the Pif1 helicase border= 
 
Tomas Lama-Diaz, Miguel G Blanco
 
 
 
The p21CIP1-CDK4-DREAM axis is a master regulator of genotoxic stress-induced cellular senescence border= 
 
Ariane Schmidt, Sebastian Allmann, Christian Schwarzenbach, Petra Snyder, Jia-Xuan Chen ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
The BRCA2 R2645G variant increases DNA binding and induces hyper-recombination border= 
 
Lucia Alvaro-Aranda, Ambre Petitalot, Yasmina Djeghmoum, Davide Panigada, Jenny Kaur Singh ...
 
 
 
Dysregulated DnaB unwinding induces replisome decoupling and daughter strand gaps that are countered by RecA polymerization border= 
 
Megan S Behrmann, Himasha M Perera, Malisha U Welikala, Jacquelynn E Matthews, Lauren J Butterworth ...
 
 
 
The loss of DNA polymerase epsilon accessory subunits POLE3'POLE4 leads to BRCA1-independent PARP inhibitor sensitivity border= 
 
Hasan Mamar, Roberta Fajka-Boja, Mónika Mórocz, Eva Pinto Jurado, Siham Zentout ...
 
 
 
Concurrent D-loop cleavage by Mus81 and Yen1 yields half-crossover precursors border=  
 
Raquel Carreira, Tomas Lama-Diaz, Maria Crugeiras, F Javier Aguado, Marek Sebesta ...
 
 
 
The translocation activity of Rad54 reduces crossover outcomes during homologous recombination border= 
 
Krishay Sridalla, Mitchell V Woodhouse, Jingyi Hu, Jessica Scheer, Bryan Ferlez ...
 
 
 
Genomics
 
 
 
 
Pseudogenes in plasmid genomes reveal past transitions in plasmid mobility border= 
 
Dustin M Hanke, Yiqing Wang, Tal Dagan
 
 
 
PHF2 regulates genome topology and DNA replication in neural stem cells via cohesin border= 
 
Jia Feng, You Heng Chuah, Yajing Liang, Nadia Omega Cipta, Yingying Zeng ...
 
 
 
Molecular Biology
 
 
 
 
Maf1 phosphorylation is regulated through the action of prefoldin-like Bud27 on PP4 phosphatase in Saccharomyces cerevisiae border= 
 
Francisco Gutiérrez-Santiago, Verónica Martínez-Fernández, Ana Isabel Garrido-Godino, Cristina Colino-Palomino, Andrés Clemente-Blanco ...
 
 
 
Primordial aminoacyl-tRNA synthetases preferred minihelices to full-length tRNA border= 
 
Guo Qing Tang, Hao Hu, Jordan Douglas, Charles W Carter, Jr
 
 
 
The activity of CobB1 protein deacetylase contributes to nucleoid compaction in Streptomyces venezuelae spores by increasing HupS affinity for DNA border= 
 
Julia DuÅ‚awa-Kobeluszczyk, Agnieszka StrzaÅ‚ka, MichaÅ‚ Tracz, Magdalena BartyÅ"ska, Katarzyna Pawlikiewicz ...
 
 
 
Bioinformatic analysis of type III CRISPR systems reveals key properties and new effector families border= 
 
Ville Hoikkala, Shirley Graham, Malcolm F White
 
 
 
Nucleic Acid Enzymes
 
 
 
 
Structural and functional investigation of the DHH/DHHA1 family proteins in Deinococcus radiodurans border= 
 
Ying Wang, Wanshan Hao, Ziming Guo, Yiyang Sun, Yu Wu ...
 
 
 
Adaptation of a eukaryote-like ProRS to a prokaryote-like tRNAPro border=  
 
Indira Rizqita Ivanesthi, Emi Latifah, Luqman Fikri Amrullah, Yi-Kuan Tseng, Tsung-Hsien Chuang ...
 
 
 
RNA and RNA-protein complexes
 
 
 
 
Massively parallel identification of sequence motifs triggering ribosome-associated mRNA quality control border= 
 
Katharine Y Chen, Heungwon Park, Arvind Rasi Subramaniam
 
 
 
The RBPome of influenza A virus NP-mRNA reveals a role for TDP-43 in viral replication border= 
 
Maud Dupont, Tim Krischuns, Quentin Giai Gianetto, Sylvain Paisant, Stefano Bonazza ...
 
 
 
Epigenetic control of adaptive or homeostatic splicing during interval-training activities border= 
 
Ling Liu, Hai Nguyen, Urmi Das, Samuel Ogunsola, Jiankun Yu ...
 
 
 
PRMT5-mediated arginine methylation of FXR1 is essential for RNA binding in cancer cells border= 
 
Anitha Vijayakumar, Mrinmoyee Majumder, Shasha Yin, Charles Brobbey, Joseph Karam ...
 
 
 
A nematode-specific ribonucleoprotein complex mediates interactions between the major nematode spliced leader snRNP and its target pre-mRNAs border= 
 
Peter Eijlers, Mohammed Al-Khafaji, Eva Soto-Martin, Rotimi Fasimoye, David Stead ...
 
 
 
Increased PTCHD4 expression via m6A modification of PTCHD4 mRNA promotes senescent cell survival 
 
Martina Rossi, Nirad Banskota, Chang Hoon Shin, Carlos Anerillas, Dimitrios Tsitsipatis ...
 
 
 
Molecular mechanism for target RNA recognition and cleavage of Cas13h border=  
 
Fugen Chen, Chendi Zhang, Jialin Xue, Feng Wang, Zhuang Li
 
 
 
Structural Biology
 
 
 
 
Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM border= 
 
Emil Gustavsson, Kay Grünewald, Per Elias, B Martin Hällberg
 
 
 
Structural characterization of two prototypical repressors of SorC family reveals tetrameric assemblies on DNA and mechanism of function border= 
 
Markéta Å oltysová, Jana Å kerlová, Petr Pachl, Karel Å kubník, Milan Fábry ...
 
 
 
Insights into the molecular mechanism of ParABS system in chromosome partition by HpParA and Hp ParB border= 
 
Chen-Hsi Chu, Che-Ting Wu, Min-Guan Lin, Cheng-Yi Yen, Yi-Zhan Wu ...
 
 
 
DMC1 and RAD51 bind FxxA and FxPP motifs of BRCA2 via two separate interfaces border=  
 
Simona Miron, Pierre Legrand, Pauline Dupaigne, Sari E van Rossum-Fikkert, Dejan Ristic ...
 
 
 
Structure of the E. coli nucleoid-associated protein YejK reveals a novel DNA binding clamp border= 
 
Maria A Schumacher, Rajiv R Singh, Raul Salinas
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
LowTempGAL: a highly responsive low temperature-inducible GAL system in Saccharomyces cerevisiae border= 
 
Zeyu Lu, Qianyi Shen, Naga Chandra Bandari, Samuel Evans, Liam McDonnell ...
 
 
 
Modular CRISPR/Cas12a synergistic activation platform for detection and logic operations border= 
 
Minghao Hu, Xianzhi Cheng, Tongbo Wu
 
 
 
Corrections
 
 
 
 
Correction to ˜The BRCA2 R2645G variant increases DNA binding and induces hyper-recombination' border= 
 
 
 
 
Correction to ˜MCPIP1 ribonuclease exhibits broad-spectrum antiviral effects through viral RNA binding and degradation' border= 
 
 
 
 
Methods
 
 
 
 
Liam tackles complex multimodal single-cell data integration challenges border= 
 
Pia Rautenstrauch, Uwe Ohler
 
 
 
mosaicMPI: a framework for modular data integration across cohorts and -omics modalities border= 
 
Theodore B Verhey, Heewon Seo, Aaron Gillmor, Varsha Thoppey-Manoharan, David Schriemer ...
 
 
 
Biochemical properties of chromatin domains define genome compartmentalization border= 
 
Federica Lucini, Cristiano Petrini, Elisa Salviato, Koustav Pal, Valentina Rosti ...
 
 
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