Subject: Nucleic Acids Research Table of Contents for 8 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 8
 
8 May 2024
 
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EditorialCritical Reviews and Perspectives
 
 
 
 
Critical steps in the assembly process of the bacterial 50S ribosomal subunit border= 
 
Amal Seffouh, Rainer Nikolay, Joaquin Ortega
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
The diversity of splicing modifiers acting on A-1 bulged 5-splice sites reveals rules for rational drug design border= 
 
Florian Malard, Antje C Wolter, Julien Marquevielle, Estelle Morvan, Agathe Ecoutin ...
 
 
 
Computational Biology
 
 
 
 
Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation border= 
 
Nanjun Chen, Jixiang Yu, Zhe Liu, Lingkuan Meng, Xiangtao Li ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
Chromatin damage generated by DNA intercalators leads to degradation of RNA Polymerase II border= 
 
Jaime A Espinoza, Dimitris C Kanellis, Sheetanshu Saproo, Karla Leal, Johana Fernandez Martinez ...
 
 
 
Differential expression of paralog RNA binding proteins establishes a dynamic splicing program required for normal cerebral cortex development border= 
 
Eleonora Cesari, Donatella Farini, Vanessa Medici, Ingrid Ehrmann, Marika Guerra ...
 
 
 
 
Activation of zinc uptake regulator by zinc binding to three regulatory sites border= 
 
Yunchan Choi, Junseock Koh, Sun-Shin Cha, Jung-Hye Roe
 
 
 
Set2 regulates Ccp1 and Swc2 to ensure centromeric stability by retargeting CENP-A border= 
 
Kim Kiat Lim, Ulysses Tsz Fung Lam, Ying Li, Yi Bing Zeng, Henry Yang ...
 
 
 
Leveraging chromatin state transitions for the identification of regulatory networks orchestrating heart regeneration border= 
 
Julio Cordero, Adel Elsherbiny, Yinuo Wang, Lonny Jürgensen, Florian Constanty ...
 
 
 
Lineage-determining transcription factor-driven promoters regulate cell type-specific macrophage gene expression border= 
 
Gergely Nagy, Dóra Bojcsuk, Petros Tzerpos, Tímea Cseh, László Nagy
 
 
 
Zebrafish Mbd5 binds to RNA m5 C and regulates histone deubiquitylation and gene expression in development metabolism and behavior border= 
 
Jianhua Guo, Zhongyu Zou, Xiaoyang Dou, Xiang Zhao, Yimin Wang ...
 
 
 
 
Phylogeny-linked occurrence of ribosome stalling on the mRNAs of Arabidopsis unfolded protein response factor bZIP60 orthologs in divergent plant species border= 
 
Tomoya Imamichi, Nao Kusumoto, Haruka Aoyama, Seidai Takamatsu, Yugo Honda ...
 
 
 
Novel insights into the role of translesion synthesis polymerase in DNA incorporation and bypass of 5-fluorouracil in colorectal cancer border= 
 
Jameson R Averill, Jackson C Lin, John Jung, Hunmin Jung
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
DNA-PK controls Apollo's access to leading-end telomeres border= 
 
Ceylan Sonmez, Beatrice Toia, Patrik Eickhoff, Andreea Medeea Matei, Michael El Beyrouthy ...
 
 
 
Physical interaction with Spo11 mediates the localisation of Mre11 to chromatin in meiosis and promotes its nuclease activity border= 
 
Rakesh Aithal, Kuldeep Nangalia, Mario Spirek, Doris Chen, Franz Klein ...
 
 
 
The origin recognition complex requires chromatin tethering by a hypervariable intrinsically disordered region that is functionally conserved from sponge to man border= 
 
Olubu A Adiji, Brendan S McConnell, Matthew W Parker
 
 
 
Pathogenic CANVAS (AAGGG)n repeats stall DNA replication due to the formation of alternative DNA structures border= 
 
Julia A Hisey, Elina A Radchenko, Nicholas H Mandel, Ryan J McGinty, Gabriel Matos-Rodrigues ...
 
 
 
COSA-1 mediated pro-crossover complex formation promotes meiotic crossing over in C. elegans border= 
 
Yuejun Yang, Nan Wang, Guoteng Liu, Wencong Nan, Bin Wang ...
 
 
 
Genomics
 
 
 
 
Mutation rate heterogeneity at the sub-gene scale due to local DNA hypomethylation border= 
 
David Mas-Ponte, Fran Supek
 
 
 
Discovery of a polymorphic gene fusion via bottom-up chimeric RNA prediction border=  
 
Justin Elfman, Lynette Goins, Tessa Heller, Sandeep Singh, Yuh-Hwa Wang ...
 
 
 
Molecular Biology
 
 
 
 
BRD2 promotes antibody class switch recombination by facilitating DNA repair in collaboration with NIPBL border= 
 
Santosh K Gothwal, Ahmed M Refaat, Mikiyo Nakata, Andre Stanlie, Tasuku Honjo ...
 
 
 
A phage nucleus-associated RNA-binding protein is required for jumbo phage infection border= 
 
Eray Enustun, Emily G Armbruster, Jina Lee, Sitao Zhang, Brian A Yee ...
 
 
 
Bridging DNA contacts allow Dps from E. coli to condense DNA border=  
 
Sneha Shahu, Natalia Vtyurina, Moumita Das, Anne S Meyer, Mahipal Ganji ...
 
 
 
The effect of pseudoknot base pairing on cotranscriptional structural switching of the fluoride riboswitch border= 
 
Laura M Hertz, Elise N White, Konstantin Kuznedelov, Luyi Cheng, Angela M Yu ...
 
 
 
Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter border= 
 
Zuyao Ni, Nujhat Ahmed, Syed Nabeel-Shah, Xinghua Guo, Shuye Pu ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
Determinants of CRISPR Cas12a nuclease activation by DNA and RNA targets border= 
 
Eric A Nalefski, Remy M Kooistra, Ishira Parikh, Samantha Hedley, Karunya Rajaraman ...
 
 
 
Molecular basis of A. thaliana KEOPS complex in biosynthesizing tRNA t6 A border= 
 
Xinxing Zheng, Chenchen Su, Lei Duan, Mengqi Jin, Yongtao Sun ...
 
 
 
Biochemical characterization of the meiosis-essential yet evolutionarily divergent topoisomerase VIB-like protein MTOPVIB from Arabidopsis thaliana border= 
 
Hsin-Wen Chen, Hsin-Yi Yeh, Chih-Chiang Chang, Wei-Chen Kuo, Sheng-Wei Lin ...
 
 
 
RNA polymerase SI3 domain modulates global transcriptional pausing and pause-site fluctuations border= 
 
Yu Bao, Xinyun Cao, Robert Landick
 
 
 
RNA and RNA-protein complexes
 
 
 
 
Temperature-sensitive splicing defects in Arabidopsis mitochondria caused by mutations in the ROOT PRIMORDIUM DEFECTIVE 1 gene border= 
 
Chuande Wang, Martine Quadrado, Hakim Mireau
 
 
 
All exons are not created equal'exon vulnerability determines the effect of exonic mutations on splicing border= 
 
Lise L Holm, Thomas K Doktor, Katharina K Flugt, Ulrika S S Petersen, Rikke Petersen ...
 
 
 
RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria border= 
 
Viola Vaňková Hausnerová, Mahmoud Shoman, Dilip Kumar, Marek Schwarz, Martin Modrák ...
 
 
 
Ribosomal collision is not a prerequisite for ZNF598-mediated ribosome ubiquitination and disassembly of ribosomal complexes by ASCC border= 
 
Anna Miścicka, Alexander G Bulakhov, Kazushige Kuroha, Alexandra Zinoviev, Christopher U T Hellen ...
 
 
 
Landscape of RNA pseudouridylation in archaeon Sulfolobus islandicus border=  
 
Yuqian Li, Songlin Wu, Keqiong Ye
 
 
 
Structural Biology
 
 
 
 
The crystal structure of bacteriophage lambda RexA provides novel insights into the DNA binding properties of Rex-like phage exclusion proteins border= 
 
Myfanwy C Adams, Carl J Schiltz, Jing Sun, Christopher J Hosford, Virginia M Johnson ...
 
 
 
Unearthing a novel function of SRSF1 in binding and unfolding of RNA G-quadruplexes border= 
 
Naiduwadura Ivon Upekala De Silva, Nathan Lehman, Talia Fargason, Trenton Paul, Zihan Zhang ...
 
 
 
Resolving the intricate binding of neomycin B to multiple binding motifs of a neomycin-sensing riboswitch aptamer by native top-down mass spectrometry and NMR spectroscopy border= 
 
Sarah Viola Heel, Fabian Juen, Karolina Bartosik, Ronald Micura, Christoph Kreutz ...
 
 
 
Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation border= 
 
Bikash R Sahoo, Vojč Kocman, Nathan Clark, Nikhil Myers, Xiexiong Deng ...
 
 
 
Structure-functional characterization of Lactococcus AbiA phage defense system border= 
 
Marta Gapi"ska, Weronika Zajko, Krzysztof Skowronek, Małgorzata Figiel, Paweł S Krawczyk ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
Multiplexed in-situ mutagenesis driven by a dCas12a-based dual-function base editor border= 
 
Yaokang Wu, Yang Li, Yanfeng Liu, Xiang Xiu, Jiaheng Liu ...
 
 
 
Correction
 
 
 
 
Correction to Non-CpG methylation by DNMT3B facilitates REST binding and gene silencing in developing mouse hearts' border= 
 
 
 
 
Correction to SomaMutDB: a database of somatic mutations in normal human tissues' border= 
 
 
 
 
Correction to POT-3 preferentially binds the terminal DNA-repeat on the telomeric G-overhang' border= 
 
 
 
 
Methods
 
 
 
 
Live-cell imaging of human apurinic/apyrimidinic endonuclease 1 in the nucleus and nucleolus using a chaperone@DNA probe border= 
 
Xiangjian Cao, Jinghui Zheng, Ruilan Zhang, Ying Sun, Meiping Zhao
 
 
 
txtools: an R package facilitating analysis of RNA modifications, structures, and interactions border= 
 
Miguel Angel Garcia-Campos, Schraga Schwartz
 
 
 
ORBIT for E. coli : kilobase-scale oligonucleotide recombineering at high throughput and high efficiency border= 
 
Scott H Saunders, Ayesha M Ahmed
 
 
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