Subject: Nucleic Acids Research Table of Contents for 12 August 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 14
 
12 August 2024
 
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NAR Breakthrough Article
 
 
 
 
Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD border= 
 
Xiaocen Lu, Luiz F M Passalacqua, Matthew Nodwell, Kristen Y S Kong, Guillermo Caballero-García ...
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
iMab antibody binds single-stranded cytosine-rich sequences and unfolds DNA i-motifs border= 
 
Joseph Boissieras, Hugues Bonnet, Maria Fidelia Susanto, Dennis Gomez, Eric Defrancq ...
 
 
 
DNA-controlled protein fluorescence: Design of aptamer-split peptide hetero-modulator for GFP to respond to intracellular ATP levels border= 
 
Ki Sung Park, Hanvit Cha, Jia Niu, Hyongsok Tom Soh, Jin Hyup Lee ...
 
 
 
Aptamer binding footprints discriminate alpha -synuclein fibrillar polymorphs from different synucleinopathies border= 
 
Alix Bouvier-Müller, Deborah Fourmy, Alexis Fenyi, Luc Bousset, Ronald Melki ...
 
 
 
Computational Biology
 
 
 
 
Machine learning enables pan-cancer identification of mutational hotspots at persistent CTCF binding sites border= 
 
Wenhan Chen, Yi C Zeng, Joanna Achinger-Kawecka, Elyssa Campbell, Alicia K Jones ...
 
 
 
 
Assessing the impact of transcriptomics data analysis pipelines on downstream functional enrichment results border= 
 
Victor Paton, Ricardo Omar Ramirez Flores, Attila Gabor, Pau Badia-i-Mompel, Jovan Tanevski ...
 
 
 
Evidence for widespread translation of 5² untranslated regions border=  
 
Jose Manuel Rodriguez, Federico Abascal, Daniel Cerdán-Vélez, Laura Martínez Gómez, Jesús Vázquez ...
 
 
 
Data Resources and Analyses
 
 
 
 
CilioGenics: an integrated method and database for predicting novel ciliary genes border= 
 
Mustafa S Pir, Efe Begar, Ferhan Yenisert, Hasan C Demirci, Mustafa E Korkmaz ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
The relationship between nanoscale genome organization and gene expression in mouse embryonic stem cells during pluripotency transition border= 
 
Ximena Garate, Pablo Aurelio Gómez-García, Manuel Fernández Merino, Marta Cadevall Angles, Chenggan Zhu ...
 
 
 
Increased transcriptional elongation and RNA stability of GPCR ligand binding genes unveiled via RNA polymerase II degradation border= 
 
Lijun Bao, Junyi Zhu, Tingxin Shi, Yongpeng Jiang, Boyuan Li ...
 
 
 
 
Loops are geometric catalysts for DNA integration border= 
 
Cleis Battaglia, Davide Michieletto
 
 
 
Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending border= 
 
Yimin Hu, Samuel Schwab, Silvia Deiss, Pedro Escudeiro, Thor van Heesch ...
 
 
 
Efficient activation of hundreds of LTR12C elements reveals cis -regulatory function determined by distinct epigenetic mechanisms border= 
 
Hitoshi Ohtani, Minmin Liu, Gangning Liang, H Josh Jang, Peter A Jones
 
 
 
HDAC4 influences the DNA damage response and counteracts senescence by assembling with HDAC1/HDAC2 to control H2BK120 acetylation and homology-directed repair border= 
 
Eros Di Giorgio, Emiliano Dalla, Vanessa Tolotto, Francesca D'Este, Harikrishnareddy Paluvai ...
 
 
 
Staphylococcal aconitase expression during iron deficiency is controlled by an sRNA-driven feedforward loop and moonlighting activity border= 
 
Maxime Barrault, Svetlana Chabelskaya, Rodrigo H Coronel-Tellez, Claire Toffano-Nioche, Eric Jacquet ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
ASH1L guards cis -regulatory elements against cyclobutane pyrimidine dimer induction border= 
 
Michelle N Yancoskie, Reihaneh Khaleghi, Anirvinya Gururajan, Aadarsh Raghunathan, Aryan Gupta ...
 
 
 
Distinct DNA repair mechanisms prevent formaldehyde toxicity during development, reproduction and aging border= 
 
Matthias Rieckher, Christian Gallrein, Natividad Alquezar-Artieda, Nour Bourached-Silva, Pavana Lakshmi Vaddavalli ...
 
 
 
SUMO protease and proteasome recruitment at the nuclear periphery differently affect replication dynamics at arrested forks border= 
 
Kamila Schirmeisen, Karel Naiman, Karine Fréon, Laetitia Besse, Shrena Chakraborty ...
 
 
 
DNA binding and bridging by human CtIP in the healthy and diseased states border=  
 
Shreya Lokanathan Balaji, Sara De Bragança, Francisco Balaguer-Pérez, Sarah Northall, Oliver John Wilkinson ...
 
 
 
MRNIP limits ssDNA gaps during replication stress border=  
 
Laura G Bennett, Ellen G Vernon, Vithursha Thanendran, Caryl M Jones, Amelia Gamble ...
 
 
 
Distinct mobility patterns of BRCA2 molecules at DNA damage sites border=  
 
Maarten W Paul, Jesse Aaron, Eric Wait, Romano M Van Genderen, Arti Tyagi ...
 
 
 
Genomics
 
 
 
 
Rapid functional activation of horizontally transferred eukaryotic intron-containing genes in the bacterial recipient border= 
 
Wen Yuan, Jing Yu, Zhichao Li
 
 
 
Molecular Biology
 
 
 
 
Principles of miRNA/miRNA* function in plant MIRNA processing border= 
 
Santiago Rosatti, Arantxa M L Rojas, Belén Moro, Irina P Suarez, Nicolas G Bologna ...
 
 
 
A new anti-CRISPR gene promotes the spread of drug-resistance plasmids in Klebsiella pneumoniae border= 
 
Chunyu Jiang, Chengzhi Yu, Shuyi Sun, Jiajia Lin, Mufeng Cai ...
 
 
 
Phase-separated ParB enforces diverse DNA compaction modes and stabilizes the parS-centered partition complex border= 
 
Yilin Zhao, Lijuan Guo, Jiaojiao Hu, Zhiyun Ren, Yanan Li ...
 
 
 
TMPyP binding evokes a complex, tunable nanomechanical response in DNA border=  
 
Balázs Kretzer, Levente Herényi, Gabriella Csík, Eszter Supala, Ádám Orosz ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
Structural insight into the Csx1'Crn2 fusion self-limiting ribonuclease of type III CRISPR system border= 
 
Danping Zhang, Liyang Du, Haishan Gao, Cai Yuan, Zhonghui Lin
 
 
 
Structure analysis of the telomere resolvase from the Lyme disease spirochete Borrelia garinii reveals functional divergence of its C-terminal domain border= 
 
Cameron Semper, Nobuhiko Watanabe, Elina Karimullina, Deepak T Patel, Rosa Di Leo ...
 
 
 
DNA-terminus-dependent transcription by T7 RNA polymerase and its C-helix mutants border= 
 
Bingbing Yu, Yifan Chen, Yan Yan, Xueling Lu, Bin Zhu
 
 
 
RNA and RNA-protein complexes
 
 
 
 
Structure-based characterization and compound identification of the wild-type THF class-II riboswitch border= 
 
Chunyan Li, Xiaochen Xu, Zhi Geng, Luqian Zheng, Qianqian Song ...
 
 
 
Arabidopsis AGO1 N-terminal extension acts as an essential hub for PRMT5 interaction and post-translational modifications border= 
 
Andrea Martín-Merchán, Antonela Lavatelli, Camila Engler, Víctor M González-Miguel, Belén Moro ...
 
 
 
A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis border= 
 
Hiraku Takada, Helge Paternoga, Keigo Fujiwara, Jose A Nakamoto, Esther N Park ...
 
 
 
Recruitment of multi-segment genomic RNAs by Bluetongue virus requires a preformed RNA network border= 
 
Po-yu Sung, Jody E Phelan, Dongsheng Luo, Raghavendran Kulasegaran-Shylini, Patrick Bohn ...
 
 
 
A high-resolution map of functional miR-181 response elements in the thymus reveals the role of coding sequence targeting and an alternative seed match border= 
 
Nikita A Verheyden, Melina Klostermann, Mirko Brüggemann, Hanna M Steede, Anica Scholz ...
 
 
 
Parsing the roles of DExD-box proteins DDX39A and DDX39B in alternative RNA splicing border= 
 
Shefali Banerjee, Chloe K Nagasawa, Steven G Widen, Mariano A Garcia-Blanco
 
 
 
Structural Biology
 
 
 
 
Phosphorylation at the disordered N-end makes HuR accumulate and dimerize in the cytoplasm border= 
 
Blanca Baños-Jaime, Laura Corrales-Guerrero, Gonzalo Pérez-Mejías, Claudia M Rejano-Gordillo, Adrián Velázquez-Campoy ...
 
 
 
Structural basis of water-mediated cis Watson'Crick/Hoogsteen base-pair formation in non-CpG methylation border= 
 
Shan-Meng Lin, Hsiang-Ti Huang, Pei-Ju Fang, Chi-Fon Chang, Roshan Satange ...
 
 
 
Ocr-mediated suppression of BrxX unveils a phage counter-defense mechanism border=  
 
Shen Li, Tianhao Xu, Xinru Meng, Yujuan Yan, Ying Zhou ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
Logical regulation of endogenous gene expression using programmable, multi-input processing CRISPR guide RNAs border= 
 
Hansol Kang, Dongwon Park, Jongmin Kim
 
 
 
Dual genetic level modification engineering accelerate genome evolution of Corynebacterium glutamicum border= 
 
Qing Wang, Jie Zhang, Zhe Zhao, Yichen Li, Jiajia You ...
 
 
 
EcCas6e-based antisense crRNA for gene repression and RNA editing in microorganisms border= 
 
Mutong Li, Zhaohui Cai, Shucheng Song, Xinmin Yue, Wenyu Lu ...
 
 
 
Methods
 
 
 
 
Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome border= 
 
Shuai Wang, Yiqi Jiang, Lijia Che, Ruo Han Wang, Shuai Cheng Li
 
 
 
CLEMENT: genomic decomposition and reconstruction of non-tumor subclones border=  
 
Young-soo Chung, Seungseok Kang, Jisu Kim, Sangbo Lee, Sangwoo Kim
 
 
 
Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing border= 
 
Josh L Espinoza, Allan Phillips, Melanie B Prentice, Gene S Tan, Pauline L Kamath ...
 
 
 
Directed evolution of hyperactive integrases for site specific insertion of transgenes border= 
 
Brian E Hew, Sabranth Gupta, Ryuei Sato, David F Waller, Ilko Stoytchev ...
 
 
 
PBOX-sRNA-seq uncovers novel features of miRNA modification and identifies selected 5²-tRNA fragments bearing 2²-O -modification border= 
 
Susu Chen, Yuchen Cai, Huiru Yang, Bin Zhang, Ning Li ...
 
 
 
Functional analysis of protein interactions using coupled bi-fluorescence complementation/GFP nanobody techniques border= 
 
Tetsuaki Miyake, John C McDermott
 
 
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