Subject: Nucleic Acids Research Table of Contents for 27 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 15
 
27 August 2024
 
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NAR Breakthrough Article
 
 
 
 
PCAF promotes R-loop resolution via histone acetylation border= 
 
Seo Yun Lee, Soo Hyeon Lee, Nak Hun Choi, Ja Young Kim, Jun Hee Kweon ...
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
Weak-cooperative binding of a long single-stranded DNA chain on a surface border= 
 
Giovanni Nava, Thomas Carzaniga, Luca Casiraghi, Erik Bot, Giuliano Zanchetta ...
 
 
 
Nanoscale dynamics and localization of single endogenous mRNAs in stress granules border= 
 
Ko Sugawara, Shin-nosuke Uno, Mako Kamiya, Akihiko Sakamoto, Yasuteru Urano ...
 
 
 
mRNA-specific readthrough of nonsense codons by antisense oligonucleotides (R-ASOs) border= 
 
Denis Susorov, Dimas Echeverria, Anastasia Khvorova, Andrei A Korostelev
 
 
 
Site-specific N-alkylation of DNA oligonucleotide nucleobases by DNAzyme-catalyzed reductive amination border= 
 
Robert D Boyd, Morgan M Kennebeck, Aurora A Miranda, Zehui Liu, Scott K Silverman
 
 
 
 
 
Computational Biology
 
 
 
 
SigAlign: an alignment algorithm guided by explicit similarity criteria border= 
 
Kunhyung Bahk, Joohon Sung
 
 
 
Interpretable deep residual network uncovers nucleosome positioning and associated features border= 
 
Yosef Masoudi-Sobhanzadeh, Shuxiang Li, Yunhui Peng, Anna R Panchenko
 
 
 
Data Resources and Analyses
 
 
 
 
Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing border= 
 
Lu Tan, Zhihao Guo, Yanwen Shao, Lianwei Ye, Miaomiao Wang ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
Disordered sequences of transcription factors regulate genomic binding by integrating diverse sequence grammars and interaction types border= 
 
Bohdana Hurieva, Divya Krishna Kumar, Rotem Morag, Offir Lupo, Miri Carmi ...
 
 
 
Differential impact of quiescent non-coding loci on chromatin entropy border=  
 
Peiyao Wu, Mina Yao, Wei Wang
 
 
 
 
PRPF40A induces inclusion of exons in GC-rich regions important for human myeloid cell differentiation border= 
 
Cheryl Weiqi Tan, Donald Yuhui Sim, Yashu Zhen, Haobo Tian, Jace Koh ...
 
 
 
Chromatin context-dependent effects of epigenetic drugs on CRISPR-Cas9 editing border= 
 
Ruben Schep, Max Trauernicht, Xabier Vergara, Anoek Friskes, Ben Morris ...
 
 
 
Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis border= 
 
Gerardo Del Toro-De León, Joram van Boven, Juan Santos-González, Wen-Biao Jiao, Haoran Peng ...
 
 
 
Characterization of a MHYT domain-coupled transcriptional regulator that responds to carbon monoxide border= 
 
Gonzalo Durante-Rodríguez, Sofía de Francisco-Polanco, José Luis García, Eduardo Díaz
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
A RAD18'UBC13'PALB2'RNF168 axis mediates replication fork recovery in BRCA1-deficient cancer cells border= 
 
Emily Cybulla, Sierra Wallace, Alice Meroni, Jessica Jackson, Sumedha Agashe ...
 
 
 
Single-molecule characterization of SV40 replisome and novel factors: human FPC and Mcm10 border= 
 
Yujing Ouyang, Amani Al-Amodi, Muhammad Tehseen, Lubna Alhudhali, Afnan Shirbini ...
 
 
 
Nuclear F-actin assembly on damaged chromatin is regulated by DYRK1A and Spir1 phosphorylation border= 
 
Junshi Li, Nan Xiong, Kirk L West, Manton Leung, Yick Pang Ching ...
 
 
 
End resection and telomere healing of DNA double-strand breaks during nematode programmed DNA elimination border= 
 
Brandon Estrem, Richard E Davis, Jianbin Wang
 
 
 
The TOPOVIBL meiotic DSB formation protein: new insights from its biochemical and structural characterization border= 
 
Boubou Diagouraga, Izabella Tambones, Coralie Carivenc, Chérine Bechara, Marc Nadal ...
 
 
 
Genomics
 
 
 
 
Unraveling the interplay between a small RNA and RNase E in bacteria border= 
 
Meshi Barsheshet Vigoda, Liron Argaman, Mark Kournos, Hanah Margalit
 
 
 
Molecular Biology
 
 
 
 
Sequence diversity of apidaecin-like peptides arresting the terminating ribosome border= 
 
Weiping Huang, Chetana Baliga, Nora Vázquez-Laslop, Alexander S Mankin
 
 
 
Diversification of the Rho transcription termination factor in bacteria border=  
 
Sofia M Moreira, Te-yuan Chyou, Joseph T Wade, Chris M Brown
 
 
 
Staphylococcal exoribonuclease YhaM destabilizes ribosomes by targeting the mRNA of a hibernation factor border= 
 
Anna LipoÅ"ska, Hyun Lee, Mee-Ngan F Yap
 
 
 
Conformational dynamics of CasX (Cas12e) in mediating DNA cleavage revealed by single-molecule FRET border= 
 
Wenjing Xing, Danyuan Li, Wenjuan Wang, Jun-Jie Gogo Liu, Chunlai Chen
 
 
 
Ribosomal protein RPL39L is an efficiency factor in the cotranslational folding of a subset of proteins with alpha helical domains border= 
 
Arka Banerjee, Meric Ataman, Maciej Jerzy Smialek, Debdatto Mookherjee, Julius Rabl ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
Aurora: a fluorescent deoxyribozyme for high-throughput screening border= 
 
Martin Volek, Jaroslav Kurfürst, MatúÅ¡ Drexler, Michal Svoboda, Pavel Srb ...
 
 
 
Apollon: a deoxyribozyme that generates a yellow product border=  
 
Martin Volek, Jaroslav Kurfürst, Milan KožíÅ¡ek, Pavel Srb, Václav Veverka ...
 
 
 
MUT-7 exoribonuclease activity and localization are mediated by an ancient domain border= 
 
Virginia Busetto, Lizaveta Pshanichnaya, Raffael Lichtenberger, Stephan Hann, René F Ketting ...
 
 
 
Single-mode termination of phage transcriptions, disclosing bacterial adaptation for facilitated reinitiations border= 
 
Eunho Song, Sun Han, Heesoo Uhm, Changwon Kang, Sungchul Hohng
 
 
 
Structural analysis of the BisI family of modification dependent restriction endonucleases border= 
 
Katarzyna Szafran, Dominik Rafalski, Krzysztof Skowronek, Marek Wojciechowski, Asgar Abbas Kazrani ...
 
 
 
RNA and RNA-protein complexes
 
 
 
 
RIL-seq reveals extensive involvement of small RNAs in virulence and capsule regulation in hypervirulent Klebsiella pneumoniae border= 
 
Kwok Jian Goh, Yael Altuvia, Liron Argaman, Yair Raz, Amir Bar ...
 
 
 
U6 snRNA m6A modification is required for accurate and efficient splicing of C. elegans and human pre-mRNAs border= 
 
Aykut Shen, Katarzyna Hencel, Matthew T Parker, Robyn Scott, Roberta Skukan ...
 
 
 
Cooperation of regulatory RNA and the RNA degradosome in transcript surveillance border= 
 
Katarzyna J Bandyra, Kathrin S Fröhlich, Jörg Vogel, Marina Rodnina, Akanksha Goyal ...
 
 
 
The fission yeast ortholog of Coilin, Mug174, forms Cajal body-like nuclear condensates and is essential for cellular quiescence border= 
 
Xiaoling Deng, Qinglian Yao, Attila Horvath, Ziling Jiang, Junjie Zhao ...
 
 
 
Concerted action of ataxin-2 and PABPC1-bound mRNA poly(A) tail in the formation of stress granules border= 
 
Ryota Yamagishi, Hiroto Inagaki, Jun Suzuki, Nao Hosoda, Haruka Sugiyama ...
 
 
 
MicroRNA biogenesis is broadly disrupted by inhibition of the splicing factor SF3B1 border= 
 
Angela Downie Ruiz Velasco, Aimee L Parsons, Matthew C Heatley, Athena R G Martin, Alfredo D Smart ...
 
 
 
TRMT10A dysfunction perturbs codon translation of initiator methionine and glutamine and impairs brain functions in mice border= 
 
Roland Tresky, Yuta Miyamoto, Yu Nagayoshi, Yasushi Yabuki, Kimi Araki ...
 
 
 
Taxonomy of introns and the evolution of minor introns border=  
 
Anouk M Olthof, Charles F Schwoerer, Kaitlin N Girardini, Audrey L Weber, Karen Doggett ...
 
 
 
Structural Biology
 
 
 
 
Cytosine analogues as DNA methyltransferase substrates border= 
 
Marek Wojciechowski, Honorata Czapinska, Joanna Krwawicz, Dominik Rafalski, Matthias Bochtler
 
 
 
DdrC, a unique DNA repair factor from D. radiodurans, senses and stabilizes DNA breaks through a novel lesion-recognition mechanism border= 
 
Robert Szabla, Mingyi Li, Victoria Warner, Yifeng Song, Murray Junop
 
 
 
Targeting DNA junction sites by bis-intercalators induces topological changes with potent antitumor effects border= 
 
Shih-Chun Huang, Chia-Wei Chen, Roshan Satange, Chang-Chih Hsieh, Chih-Chun Chang ...
 
 
 
A single CAA interrupt in a DNA three-way junction containing a CAG repeat hairpin results in parity-dependent trapping border= 
 
Gillian M Cadden, Svea J Wilken, Steven W Magennis
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
Re-engineered guide RNA enables DNA loops and contacts modulating repression in E. coli border= 
 
Yunshi Yang, Iris Rocamonde-Lago, Boxuan Shen, Ieva Berzina, Johanna Zipf ...
 
 
 
Corrections
 
 
 
 
Correction to ˜Cytosine analogues as DNA methyltransferase substrates' border= 
 
 
 
 
Correction to ˜SENEBLOC, a long non-coding RNA suppresses senescence via p53-dependent and independent mechanisms' border= 
 
 
 
 
Methods
 
 
 
 
Multiplexed sequential imaging in living cells with orthogonal fluorogenic RNA aptamer/dye pairs border= 
 
Ru Zheng, Rigumula Wu, Yuanchang Liu, Zhining Sun, Zhaolin Xue ...
 
 
 
protoSpaceJAM: an open-source, customizable and web-accessible design platform for CRISPR/Cas insertional knock-in border= 
 
Duo Peng, Madhuri Vangipuram, Joan Wong, Manuel D Leonetti
 
 
 
Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation border= 
 
Juan Mulero-Hernández, Vladimir Mironov, José Antonio Miñarro-Giménez, Martin Kuiper, Jesualdo Tomás Fernández-Breis
 
 
 
Imaging and quantification of human and viral circular RNAs border=  
 
Dabbu Kumar Jaijyan, Shaomin Yang, Santhamani Ramasamy, Alison Gu, Mulan Zeng ...
 
 
 
Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactions border= 
 
Yu Wang, Xiaoyu Liu, Yitian Zeng, Sinem K Saka, Wenxin Xie ...
 
 
 
Monitoring nucleolar-nucleoplasmic protein shuttling in living cells by high-content microscopy and automated image analysis border= 
 
Marina Engbrecht, David Grundei, Asisa M Dilger, Hannah Wiedemann, Ann-Kristin Aust ...
 
 
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