Subject: Nucleic Acids Research Table of Contents for 22 May 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 9
 
22 May 2024
 
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Critical Reviews and Perspectives
 
 
 
 
Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges border= 
 
Hung Nguyen, Ha Nguyen, Duc Tran, Sorin Draghici, Tin Nguyen
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
A novel transient receptor potential C3/C6 selective activator induces the cellular uptake of antisense oligonucleotides border= 
 
Hiroto Kohashi, Ryu Nagata, Yusuke Tamenori, Tomorrow Amatani, Yoshifumi Ueda ...
 
 
 
Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo border= 
 
Samantha L Sarli, Hassan H Fakih, Karen Kelly, Gitali Devi, Julia M Rembetsy-Brown ...
 
 
 
Computational Biology
 
 
 
 
Definition of the binding specificity of the T7 bacteriophage primase by analysis of a protein binding microarray using a thermodynamic model border= 
 
Georg Lipps
 
 
 
m6ACali: machine learning-powered calibration for accurate m6A detection in MeRIP-Seq border= 
 
Haokai Ye, Tenglong Li, Daniel J Rigden, Zhen Wei
 
 
 
 
High-density generation of spatial transcriptomics with STAGE border= 
 
Shang Li, Kuo Gai, Kangning Dong, Yiyang Zhang, Shihua Zhang
 
 
 
Genome-wide screening and functional validation of methylation barriers near promoters border= 
 
Jingmin Shu, Jaroslav Jelinek, Hai Chen, Yan Zhang, Taichun Qin ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
RNA'RNA interactions between respiratory syncytial virus and miR-26 and miR-27 are associated with regulation of cell cycle and antiviral immunity border= 
 
Sarah Ressel, Sujai Kumar, Jose Roberto Bermúdez-Barrientos, Katrina Gordon, Julia Lane ...
 
 
 
Processivity and specificity of histone acetylation by the male-specific lethal complex border= 
 
Anna E Kiss, Anuroop V Venkatasubramani, Dilan Pathirana, Silke Krause, Aline Campos Sparr ...
 
 
 
The jet-like chromatin structure defines active secondary metabolism in fungi border=  
 
Wenyong Shao, Jingrui Wang, Yueqi Zhang, Chaofan Zhang, Jie Chen ...
 
 
 
 
Tracking pairwise genomic loci by the ParB'ParS and Noc-NBS systems in living cells border= 
 
Xiaohui He, Yuxi Tan, Ying Feng, Yadong Sun, Hanhui Ma
 
 
 
HBO1 determines SMAD action in pluripotency and mesendoderm specification border=  
 
Cong Zhang, Yongli Shan, Huaisong Lin, Yanqi Zhang, Qi Xing ...
 
 
 
ATRX guards against aberrant differentiation in mesenchymal progenitor cells border=  
 
Yan Fang, Douglas Barrows, Yakshi Dabas, Thomas S Carroll, Sam Singer ...
 
 
 
WSB1/2 target chromatin-bound lysine-methylated RelA for proteasomal degradation and NF-kappa B termination border= 
 
Jie Zhang, Yuanyuan Yu, Xiuqun Zou, Yaning Du, Qiankun Liang ...
 
 
 
Catalytic residues of microRNA Argonautes play a modest role in microRNA star strand destabilization in C. elegans 
 
Kasuen Kotagama, Acadia L Grimme, Leah Braviner, Bing Yang, Rima M Sakhawala ...
 
 
 
Defining the contribution of microRNA-specific Argonautes with slicer capability in animals border= 
 
Anisha Pal, Vaishnav Vasudevan, François Houle, Michael Lantin, Katherine A Maniates ...
 
 
 
Viral reprogramming of host transcription initiation border=  
 
Nathan A Ungerleider, Claire Roberts, Tina M O'Grady, Trang T Nguyen, Melody Baddoo ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
Correction of non-random mutational biases along a linear bacterial chromosome by the mismatch repair endonuclease NucS border= 
 
Oyut Dagva, Annabelle Thibessard, Jean-Noël Lorenzi, Victor Labat, Emilie Piotrowski ...
 
 
 
DNA-PKcs suppresses illegitimate chromosome rearrangements border=  
 
Jinglong Wang, Cheyenne A Sadeghi, Richard L Frock
 
 
 
CSB and SMARCAL1 compete for RPA32 at stalled forks and differentially control the fate of stalled forks in BRCA2-deficient cells border= 
 
Nicole L Batenburg, Dana J Sowa, John R Walker, Sara N Andres, Xu-Dong Zhu
 
 
 
LC3B drives transcription-associated homologous recombination via direct interaction with R-loops border= 
 
Junghyun Yoon, Yiseul Hwang, Hansol Yun, Jee Min Chung, Soyeon Kim ...
 
 
 
SIRT2 promotes base excision repair by transcriptionally activating OGG1 in an ATM/ATR-dependent manner border= 
 
Anke Geng, Jiahui Sun, Huanyin Tang, Yang Yu, Xiyue Wang ...
 
 
 
S-phase checkpoint prevents leading strand degradation from strand-associated nicks at stalled replication forks border= 
 
Alberto Bugallo, Mar Sánchez, María Fernández-García, Mónica Segurado
 
 
 
Defective transfer of parental histone decreases frequency of homologous recombination by increasing free histone pools in budding yeast border= 
 
Srinivasu Karri, Yi Yang, Jiaqi Zhou, Quinn Dickinson, Jing Jia ...
 
 
 
Genomics
 
 
 
 
The discovery of novel noncoding RNAs in 50 bacterial genomes border= 
 
Aya Narunsky, Gadareth A Higgs, Blake M Torres, Diane Yu, Gabriel Belem de Andrade ...
 
 
 
Comprehensive profiling of L1 retrotransposons in mouse border=  
 
Xuanming Zhang, Ivana Celic, Hannah Mitchell, Sam Stuckert, Lalitha Vedula ...
 
 
 
Comprehensive genomic features indicative for Notch responsiveness border=  
 
Benedetto Daniele Giaimo, Tobias Friedrich, Francesca Ferrante, Marek Bartkuhn, Tilman Borggrefe
 
 
 
Molecular Biology
 
 
 
 
RecA-dependent or independent recombination of plasmid DNA generates a conflict with the host EcoKI immunity by launching restriction alleviation border= 
 
Mikhail Skutel, Daria Yanovskaya, Alina Demkina, Aleksandr Shenfeld, Olga Musharova ...
 
 
 
Caspase-mediated processing of TRBP regulates apoptosis during viral infection border= 
 
Keiko Shibata, Harune Moriizumi, Koji Onomoto, Yuka Kaneko, Takuya Miyakawa ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
Activity reconstitution of Kre33 and Tan1 reveals a molecular ruler mechanism in eukaryotic tRNA acetylation border= 
 
Chun-Rui Ma, Na Liu, Hong Li, Hong Xu, Xiao-Long Zhou
 
 
 
Live-cell imaging reveals the trade-off between target search flexibility and efficiency for Cas9 and Cas12a border= 
 
Lorenzo Olivi, Cleo Bagchus, Victor Pool, Ezra Bekkering, Konstantin Speckner ...
 
 
 
SARS-CoV-2 nsp15 preferentially degrades AU-rich dsRNA via its dsRNA nickase activity border= 
 
Xionglue Wang, Bin Zhu
 
 
 
RNA and RNA-protein complexes
 
 
 
 
A combinatorial approach for achieving CNS-selective RNAi border= 
 
Chantal M Ferguson, Bruno M D C Godinho, Dimas Echeverria, Matthew Hassler, Lorenc Vangjeli ...
 
 
 
Cryo-EM structure of SRP68/72 reveals an extended dimerization domain with RNA-binding activity border= 
 
Yichen Zhong, Junjie Feng, Adrian F Koh, Abhay Kotecha, Basil J Greber ...
 
 
 
RNA-binding properties orchestrate TDP-43 homeostasis through condensate formation in vivo border= 
 
Natalie M Scherer, Cindy Maurel, Matthew S Graus, Luke McAlary, Grant Richter ...
 
 
 
A Fur family protein BosR is a novel RNA-binding protein that controls rpoS RNA stability in the Lyme disease pathogen border= 
 
Sajith Raghunandanan, Raj Priya, Fuad Alanazi, Meghan C Lybecker, Paula Jean Schlax ...
 
 
 
Dynamics of miRNA accumulation during C. elegans larval development border=  
 
Smita Nahar, Lucas J Morales Moya, Jana Brunner, Gert-Jan Hendriks, Benjamin Towbin ...
 
 
 
Nuclear RNA-related processes modulate the assembly of cytoplasmic RNA granules border= 
 
Mor Angel, Eden Fleshler, Mohammad Khaled Atrash, Noa Kinor, Jennifer I C Benichou ...
 
 
 
UPF1 ATPase autoinhibition and activation modulate RNA binding kinetics and NMD efficiency 
 
Joseph H Chapman, Alice M Youle, Acadia L Grimme, Keir C Neuman, J Robert Hogg
 
 
 
Structural Biology
 
 
 
 
Biochemical and structural characterization of Fapy¢dG replication by Human DNA polymerase beta border= 
 
Shijun Gao, Peyton N Oden, Benjamin J Ryan, Haozhe Yang, Bret D Freudenthal ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
CRISPR-Cas tools for simultaneous transcription & translation control in bacteria border= 
 
Ryan A L Cardiff, Ian D Faulkner, Juliana G Beall, James M Carothers, Jesse G Zalatan
 
 
 
Correction
 
 
 
 
Correction to ˜STIM1 translocation to the nucleus protects cells from DNA damage' border= 
 
 
 
 
Retraction
 
 
 
 
Retraction of ˜Dissecting the splicing mechanism of the Drosophila editing enzyme; dADAR' border= 
 
 
 
 
Methods
 
 
 
 
NetActivity enhances transcriptional signals by combining gene expression into robust gene set activity scores through interpretable autoencoders border=  
 
Carlos Ruiz-Arenas, Irene Marín-Goñi, Liewei Wang, Idoia Ochoa, Luis A Pérez-Jurado ...
 
 
 
Examining chromatin heterogeneity through PacBio long-read sequencing of M.EcoGII methylated genomes: an m6A detection efficiency and calling bias correcting pipeline  
 
Allison F Dennis, Zhuwei Xu, David J Clark
 
 
 
SifiNet: a robust and accurate method to identify feature gene sets and annotate cells border= 
 
Qi Gao, Zhicheng Ji, Liuyang Wang, Kouros Owzar, Qi-Jing Li ...
 
 
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