Subject: Nucleic Acids Research Table of Contents for 23 September 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 17
 
23 September 2024
 
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NAR Breakthrough Article
 
 
 
 
ENL reads histone beta -hydroxybutyrylation to modulate gene transcription border= 
 
Chen Chen, Cong Chen, Aiyuan Wang, Zixin Jiang, Fei Zhao ...
 
 
 
Critical Reviews and Perspectives
 
 
 
 
CRISPR-Cas target recognition for sensing viral and cancer biomarkers border= 
 
Shadi Rahimi, Sri Renukadevi Balusamy, Haribalan Perumalsamy, Anders Ståhlberg, Ivan Mijakovic
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
Rational design of base, sugar and backbone modifications improves ADAR-mediated RNA editing border= 
 
Genliang Lu, Chikdu Shivalila, Prashant Monian, Hui Yu, Ian Harding ...
 
 
 
Template-independent synthesis and 3²-end labelling of 2²-modified oligonucleotides with terminal deoxynucleotidyl transferases border= 
 
Leping Sun, Yuming Xiang, Yuhui Du, Yangming Wang, Jiezhao Ma ...
 
 
 
Metabolic RNA labeling in non-engineered cells following spontaneous uptake of fluorescent nucleoside phosphate analogues border= 
 
Pauline Pfeiffer, Jesper R Nilsson, Audrey Gallud, Tom Baladi, Hoang-Ngoan Le ...
 
 
 
 
 
Computational Biology
 
 
 
 
Methods for constructing and evaluating consensus genomic interval sets border= 
 
Julia Rymuza, Yuchen Sun, Guangtao Zheng, Nathan J LeRoy, Maria Murach ...
 
 
 
An integrated machine-learning model to predict nucleosome architecture border=  
 
Alba Sala, Mireia Labrador, Diana Buitrago, Pau De Jorge, Federica Battistini ...
 
 
 
Network medicine-based epistasis detection in complex diseases: ready for quantum computing border= 
 
Markus Hoffmann, Julian M Poschenrieder, Massimiliano Incudini, Sylvie Baier, Amelie Fritz ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum border= 
 
Victoria A Bonnell, Yuning Zhang, Alan S Brown, John Horton, Gabrielle A Josling ...
 
 
 
The characteristics of CTCF binding sequences contribute to enhancer blocking activity border= 
 
Felice H Tsang, Rosa J Stolper, Muhammad Hanifi, Lucy J Cornell, Helena S Francis ...
 
 
 
 
The C-terminal 4CXXC-type zinc finger domain of CDCA7 recognizes hemimethylated DNA and modulates activities of chromatin remodeling enzyme HELLS border= 
 
Akeo Shinkai, Hideharu Hashimoto, Chikako Shimura, Hiroaki Fujimoto, Kei Fukuda ...
 
 
 
Genetic'epigenetic interplay in the determination of plant 3D genome organization border= 
 
Xiaoning He, Chloé Dias Lopes, Leonardo I Pereyra-Bistrain, Ying Huang, Jing An ...
 
 
 
The enhancer RNA, AANCR, regulates APOE expression in astrocytes and microglia 
 
Ma Wan, Yaojuan Liu, Dongjun Li, Ryan J Snyder, Lillian B Elkin ...
 
 
 
Meiotic chromatin-associated HSF5 is indispensable for pachynema progression and male fertility border= 
 
Chunhai Luo, Haoran Xu, Ziqi Yu, Dalin Liu, Danyang Zhong ...
 
 
 
Rapid profiling of transcription factor'cofactor interaction networks reveals principles of epigenetic regulation border= 
 
Melissa M Inge, Rebekah Miller, Heather Hook, David Bray, Jessica L Keenan ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
PHF8 facilitates transcription recovery following DNA double-strand break repair border= 
 
Jung Eun Kim, Xiyue Pan, Kwan Yiu Tse, Henry Hei Chan, Chao Dong ...
 
 
 
DNA damage-induced phosphorylation of a replicative DNA helicase results in inhibition of DNA replication through attenuation of helicase function border= 
 
Caleb Homiski, Rama Dey-Rao, Shichen Shen, Jun Qu, Thomas Melendy
 
 
 
Structures of the mitochondrial single-stranded DNA binding protein with DNA and DNA polymerase gamma  
 
Amanda A Riccio, Jonathan Bouvette, Lars C Pedersen, Shruti Somai, Robert C Dutcher ...
 
 
 
Redundant but essential functions of PARP1 and PARP2 in DNA ligase I-independent DNA replication border= 
 
Seema Khattri Bhandari, Nathaniel Wiest, Annahita Sallmyr, Ruofei Du, Alan E Tomkinson
 
 
 
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation border= 
 
Satyajeet Rao, Martin Andrs, Kaustubh Shukla, Esin Isik, Christiane König ...
 
 
 
ADARp150 counteracts whole genome duplication border=  
 
Frank van Gemert, Alexandra Drakaki, Isabel Morales Lozano, Daniël de Groot, Maud Schoot Uiterkamp ...
 
 
 
Genomics
 
 
 
 
Clinically relevant mutations in regulatory regions of metabolic genes facilitate early adaptation to ciprofloxacin in Escherichia coli border= 
 
Arijit Pal, Dipannita Ghosh, Pratyusha Thakur, Priya Nagpal, Madhumathi Irulappan ...
 
 
 
Molecular and Structural Biology
 
 
 
 
Efficient circularization of protein-encoding RNAs via a novel cis -splicing system border= 
 
Shaojun Qi, Huiming Wang, Guopeng Liu, Qianshan Qin, Peng Gao ...
 
 
 
Molecular Biology
 
 
 
 
Transposition with Tn3 -family elements occurs through interaction with the host beta -sliding clamp processivity factor border= 
 
Yu Tang, Jianfeng Zhang, Jiahao Guan, Wei Liang, Michael T Petassi ...
 
 
 
A phage satellite manipulates the viral DNA packaging motor to inhibit phage and promote satellite spread border= 
 
Caroline M Boyd, Kimberley D Seed
 
 
 
Efficacy, biodistribution and safety comparison of chemically modified antisense oligonucleotides in the retina border= 
 
Irene Vázquez-Domínguez, Alejandro Allo Anido, Lonneke Duijkers, Tamara Hoppenbrouwers, Anita D M Hoogendoorn ...
 
 
 
Systematic discovery of DNA-binding tandem repeat proteins border=  
 
Xiaoxuan Hu, Xuechun Zhang, Wen Sun, Chunhong Liu, Pujuan Deng ...
 
 
 
The molecular mechanism for TERRA recruitment and annealing to telomeres border=  
 
Bersabel Wondimagegnhu, Wen Ma, Tapas Paul, Ting-Wei Liao, Chun Ying Lee ...
 
 
 
Novel function of U7 snRNA in the repression of HERV1/LTR12s and lincRNAs in human cells border= 
 
Patrycja Plewka, Michal W Szczesniak, Agata Stepien, Robert Pasieka, Elzbieta Wanowska ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
The SAVED domain of the type III CRISPR protease CalpL is a ring nuclease border= 
 
Sophie C Binder, Niels Schneberger, Maximilian Schmitz, Marianne Engeser, Matthias Geyer ...
 
 
 
Chemical synthesis of 2³OMeNAD+ and its deployment as an RNA 2²-phosphotransferase (Tpt1) ˜poison' that traps the enzyme on its abortive RNA-2²-PO4 -(ADP-2³OMe-ribose) reaction intermediate border= 
 
Jakob Arnold, Shreya Ghosh, Renata Kasprzyk, Marcel Brakonier, Markus Hanna ...
 
 
 
RudS: bacterial desulfidase responsible for tRNA 4-thiouridine de-modification border= 
 
Rapolas Jamontas, Audrius LaurynÄ-nas, DeimantÄ- PovilaitytÄ-, Rolandas MeÅ¡kys, Agota AuÄynaitÄ-
 
 
 
Structural basis of Cas3 activation in type I-C CRISPR-Cas system border=  
 
Do Yeon Kim, So Yeon Lee, Hyun Ji Ha, Hyun Ho Park
 
 
 
RNA and RNA-protein complexes
 
 
 
 
tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development border= 
 
Tom Rappol, Maria Waldl, Anastasia Chugunova, Ivo L Hofacker, Andrea Pauli ...
 
 
 
Cas9 interaction with the tracrRNA nexus modulates the repression of type II-A CRISPR-cas genes border= 
 
Hyejin Kim, Luciano A Marraffini
 
 
 
A new approach to RNA synthesis: immobilization of stably and functionally co-tethered promoter DNA and T7 RNA polymerase border= 
 
Kithmie MalagodaPathiranage, Ruptanu Banerjee, Craig T Martin
 
 
 
Molecular basis for cA6 synthesis by a type III-A CRISPR'Cas enzyme and its conversion to cA4 production border= 
 
Hemant N Goswami, Fozieh Ahmadizadeh, Bing Wang, Doreen Addo-Yobo, Yu Zhao ...
 
 
 
High resolution landscape of ribosomal RNA processing and surveillance border=  
 
Weidong An, Yunxiao Yan, Keqiong Ye
 
 
 
Trypanosome mRNA recapping is triggered by hypermethylation originating from cap 4 border= 
 
Anna V Ignatochkina, Jesavel A Iguchi, Anilkumar R Kore, C Kiong Ho
 
 
 
A novel interaction between the 5² untranslated region of the Chikungunya virus genome and Musashi RNA binding protein is essential for efficient virus genome replication border= 
 
Kaiwen Sun, Francesca Appadoo, Yuqian Liu, Marietta Müller, Catriona Macfarlane ...
 
 
 
The RNA helicase DDX39 contributes to the nuclear export of spliceosomal U snRNA by loading of PHAX onto RNA border= 
 
Ichiro Taniguchi, Tetsuro Hirose, Mutsuhito Ohno
 
 
 
Structural Biology
 
 
 
 
N-terminal domain of polypyrimidine-tract binding protein is a dynamic folding platform for adaptive RNA recognition border= 
 
Fred F Damberger, Miroslav Krepl, Rajika Arora, Irene Beusch, Christophe Maris ...
 
 
 
Structural insights into RNA cleavage by a novel family of bacterial RNases border=  
 
Ruoxi Wu, Shakti Ingle, Sarah A Barnes, Heather R Dahlin, Susmita Khamrui ...
 
 
 
Cryo-EM structure of DNA polymerase of African swine fever virus border=  
 
Lu Kuai, Junqing Sun, Qi Peng, Xuejin Zhao, Bin Yuan ...
 
 
 
Correction
 
 
 
 
Correction to ˜DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum' border= 
 
 
 
 
Methods
 
 
 
 
Discovery of numerous novel Helitron-like elements in eukaryote genomes using HELIANO border= 
 
Zhen Li, Clément Gilbert, Haoran Peng, Nicolas Pollet
 
 
 
Y-switch: a spring-loaded synthetic gene switch for robust DNA/RNA signal amplification and detection border= 
 
Krishna Gupta, Elisha Krieg
 
 
 
Advancing quantitative PCR with color cycle multiplex amplification border=  
 
Wei Chen, Kerou Zhang, Fei Huang, Lan Zhao, George C Waldren ...
 
 
 
Improved sub-genomic RNA prediction with the ARTIC protocol border=  
 
Thomas Baudeau, Kristoffer Sahlin
 
 
 
Invention of circRNA promoting RNA to specifically promote circRNA production border=  
 
Zhilin He, Haofei Ji, Bei Xia, Xiuen Cao, Ying Huang ...
 
 
 
NucleoFind : a deep-learning network for interpreting nucleic acid electron density border= 
 
Jordan S Dialpuri, Jon Agirre, Kathryn D Cowtan, Paul S Bond
 
 
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