Subject: Nucleic Acids Research Table of Contents for 11 December 2024 Oxford Academic
 
 
 
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NAR Invites Submissions for the 2025 Web Server Issue
 

In July of each year, NAR devotes a single issue to papers describing web-based software resources of value to the biological community. This issue focuses on web servers offering computations for DNA, RNA, and protein sequences, high-throughput sequencing data, and biological network analysis, and includes a special section for Web Services. The deadline for submitting your proposal is 20th December. 

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Nucleic Acids Research  
Volume 52 Issue 22
 
11 December 2024
 
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Editorial
 
 
 
 
Chromatin and transcription in Nucleic Acids Research: the first 50 years border= 
 
Pierre-Antoine Defossez
 
 
 
NAR Breakthrough Article
 
 
 
 
AcrIIIA1 is a protein'RNA anti-CRISPR complex that targets core Cas and accessory nucleases border= 
 
Lucy Chou-Zheng, Olivia Howell, Tori A Boyle, Motaher Hossain, Forrest C Walker ...
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
Overcoming nucleotide bias in the nonenzymatic copying of RNA templates border= 
 
Daniel Duzdevich, Christopher E Carr, Ben W F Colville, Harry R M Aitken, Jack W Szostak
 
 
 
Profiling of i-motif-binding proteins reveals functional roles of nucleolin in regulation of high-order DNA structures border= 
 
Yuki Ban, Yuka Ando, Yuma Terai, Risa Matsumura, Keita Nakane ...
 
 
 
Selective recognition of RNA G-quadruplex in vitro and in cells by L-aptamer'D-oligonucleotide conjugate border= 
 
Haizhou Zhao, Hill Lam Lau, Kun Zhang, Chun Kit Kwok
 
 
 
 
Single-stranded DNA with internal base modifications mediates highly efficient knock-in in primary cells using CRISPR-Cas9 border= 
 
Karen L Kanke, Rachael E Rayner, Jack Bozik, Eli Abel, Aparna Venugopalan ...
 
 
 
Glucose binds and activates NSUN2 to promote translation and epidermal differentiation border= 
 
Weili Miao, Douglas F Porter, Ya Li, Lindsey M Meservey, Yen-Yu Yang ...
 
 
 
Molecular basis of the phosphorothioation-sensing antiphage defense system IscS'DndBCDE'DndI border= 
 
Yaqian Tang, Dan Wu, Yueying Zhang, Xuan Liu, Hui Chu ...
 
 
 
Computational Biology
 
 
 
 
Interrogation of the interplay between DNA N6 -methyladenosine (6mA) and hypoxia-induced chromatin accessibility by a randomized empirical model (EnrichShuf) border= 
 
Joseph Chieh-Yu Lai, Kai-Wen Hsu, Kou-Juey Wu
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
The conformation of FOXM1 homodimers in vivo is crucial for regulating transcriptional activities border= 
 
Chia-Chan Hsu, Xiang Yao, Shang-Yao Chen, Tsui-Chun Tsuo, I-Ching Wang
 
 
 
 
Epigenetic characterization of adult rhesus monkey spermatogonial stem cells identifies key regulators of stem cell homeostasis border= 
 
Rui Bi, Lin-Nuo Pan, Hao Dai, Chunli Sun, Cong Li ...
 
 
 
A systematic quantitative approach comprehensively defines domain-specific functional pathways linked to Schizosaccharomyces pombe heterochromatin regulation border= 
 
Abubakar Muhammad, Zsuzsa Sarkadi, Agnisrota Mazumder, Anissia Ait Saada, Thomas van Emden ...
 
 
 
SETDB1 activity is globally directed by H3K14 acetylation via its Triple Tudor Domain border= 
 
Thyagarajan T Chandrasekaran, Michel Choudalakis, Alexander Bröhm, Sara Weirich, Alexandra G Kouroukli ...
 
 
 
Phosphorylation-mediated disassembly of C-terminal binding protein 2 tetramer impedes epigenetic silencing of pluripotency in mouse embryonic stem cells border= 
 
Han-Teo Lee, Young Ah Kim, Sangho Lee, Ye-Eun Jung, Hanbyeol Kim ...
 
 
 
Bacterial WYL domain transcriptional repressors sense single-stranded DNA to control gene expression border= 
 
Chelsea L Blankenchip, Kevin D Corbett
 
 
 
UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation border= 
 
Rochelle L Tiedemann, Joel Hrit, Qian Du, Ashley K Wiseman, Hope E Eden ...
 
 
 
Identifying key underlying regulatory networks and predicting targets of orphan C/D box SNORD116 snoRNAs in Prader'Willi syndrome border= 
 
Rachel B Gilmore, Yaling Liu, Christopher E Stoddard, Michael S Chung, Gordon G Carmichael ...
 
 
 
Control of iron acquisition by multiple small RNAs unravels a new role for transcriptional terminator loops in gene regulation border= 
 
Eugenio Solchaga Flores, Jonathan Jagodnik, Fanny Quenette, Alexey Korepanov, Maude Guillier
 
 
 
[SNG2], a prion form of Cut4/Apc1, confers non-Mendelian inheritance of heterochromatin silencing defect in fission yeast border= 
 
Suman Sharma, Suchita Srivastava, Rudra Narayan Dubey, Poonam Mishra, Jagmohan Singh
 
 
 
Crosstalk between paralogs and isoforms influences p63-dependent regulatory element activity border= 
 
Gabriele Baniulyte, Abby A McCann, Dana L Woodstock, Morgan A Sammons
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
CRISPR knockout genome-wide screens identify the HELQ-RAD52 axis in regulating the repair of cisplatin-induced single-stranded DNA gaps border= 
 
Lindsey M Pale, Jude B Khatib, Alexandra Nusawardhana, Joshua Straka, Claudia M Nicolae ...
 
 
 
Functional and molecular insights into the role of Sae2 C-terminus in the activation of MRX endonuclease border= 
 
Chiara Vittoria Colombo, Erika Casari, Marco Gnugnoli, Flavio Corallo, Renata Tisi ...
 
 
 
CAF-1 promotes efficient PrimPol recruitment to nascent DNA for single-stranded DNA gap formation border= 
 
Joshua Straka, Jude B Khatib, Lindsey Pale, Claudia M Nicolae, George-Lucian Moldovan
 
 
 
STK39-mediated amplification of gamma -H2A.X promotes homologous recombination and contributes to PARP inhibitor resistance border= 
 
Yi Xu, Changying Li, Huan Yin, Somaira Nowsheen, Xin Xu ...
 
 
 
Genomics
 
 
 
 
Full-length direct RNA sequencing reveals extensive remodeling of RNA expression, processing and modification in aging Caenorhabditis elegans border= 
 
Erin C Schiksnis, Ian A Nicastro, Amy E Pasquinelli
 
 
 
Protein moonlighting by a target gene dominates phenotypic divergence of the Sef1 transcriptional regulatory network in yeasts border= 
 
Po-Chen Hsu, Tzu-Chiao Lu, Po-Hsiang Hung, Jun-Yi Leu
 
 
 
Molecular and Structural Biology
 
 
 
 
Dimerization of the deaminase domain and locking interactions with Cas9 boost base editing efficiency in ABE8e border= 
 
Pablo R Arantes, Xiaoyu Chen, Souvik Sinha, Aakash Saha, Amun C Patel ...
 
 
 
Circular oligomeric particles formed by Ros/MucR family members mediate DNA organization in alpha -proteobacteria border= 
 
Antonio Chaves-Sanjuan, Gianluca D'Abrosca, Veronica Russo, Bert van Erp, Alessandro Del Cont-Bernard ...
 
 
 
Chemotherapeutic agents and leucine deprivation induce codon-biased aberrant protein production in cancer border= 
 
Adva Kochavi, Remco Nagel, Pierre-Rene Körner, Onno B Bleijerveld, Chun-Pu Lin ...
 
 
 
Molecular basis for thiocarboxylation and release of Urm1 by its E1-activating enzyme Uba4 border= 
 
MikoÅ‚aj SokoÅ‚owski, Dominika Kwasna, Keerthiraju E Ravichandran, Cristian Eggers, RoÅ›cisÅ‚aw KrutyhoÅ‚owa ...
 
 
 
Bacterial Rps3 counters oxidative and UV stress by recognizing and processing AP-sites on mRNA via a novel mechanism border= 
 
Mohammad Afsar, Ankita Shukla, Faiz Ali, Rahul Kumar Maurya, Suman Bharti ...
 
 
 
L1-ORF1p nucleoprotein can rapidly assume distinct conformations and simultaneously bind more than one nucleic acid border= 
 
Ben A Cashen, M Nabuan Naufer, Michael Morse, Micah J McCauley, Ioulia Rouzina ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
CRISPR-AsCas12f1 couples out-of-protospacer DNA unwinding with exonuclease activity in the sequential target cleavage border= 
 
Xiaoxuan Song, Ziting Chen, Wenjun Sun, Hao Yang, Lijuan Guo ...
 
 
 
Transfer RNA supplementation rescues HARS deficiency in a humanized yeast model of Charcot-Marie-Tooth disease border= 
 
Sarah D P Wilhelm, Jenica H Kakadia, Aruun Beharry, Rosan Kenana, Kyle S Hoffman ...
 
 
 
Tetramerization of deoxyadenosine kinase meets the demands of a DNA replication substrate challenge in Giardia intestinalis border= 
 
Farahnaz Ranjbarian, Karim Rafie, Kasturika Shankar, Sascha Krakovka, Staffan G Svärd ...
 
 
 
Interpreting CRISPR-Cas12a enzyme kinetics through free energy change of nucleic acids border= 
 
Jiongyu Zhang, Xin Guan, Jeong Moon, Shuo Zhang, Zhengyang Jia ...
 
 
 
DNA sequence and lesion-dependent mitochondrial transcription factor A (TFAM)-DNA-binding modulates DNA repair activities and products border= 
 
Kathleen Urrutia, Yu Hsuan Chen, Jin Tang, Ta I Hung, Guodong Zhang ...
 
 
 
Nucleic Acid Therapeutics
 
 
 
 
Optimization of ACE-tRNAs function in translation for suppression of nonsense mutations border= 
 
Joseph J Porter, Wooree Ko, Emily G Sorensen, John D Lueck
 
 
 
RNA and RNA-protein complexes
 
 
 
 
Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections border= 
 
Lauren N McKinley, McCauley O Meyer, Aswathy Sebastian, Benjamin K Chang, Kyle J Messina ...
 
 
 
Single-molecule visualization of sequence-specific RNA binding by a designer PPR protein border= 
 
Nicholas Marzano, Brady Johnston, Bishnu P Paudel, Jason Schmidberger, Slobodan Jergic ...
 
 
 
Retargeting target-directed microRNA-decay sites to highly expressed viral or cellular miRNAs border= 
 
Jesus A Ortega, Ziyan Liang, Junpeng Kenny Xu, Eva Gottwein
 
 
 
Distinct interactomes of ADAR1 nuclear and cytoplasmic protein isoforms and their responses to interferon induction border= 
 
Dragana Vukić, Anna Cherian, Salla Keskitalo, Yih Tyng Bong, Martin Marônek ...
 
 
 
Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation border= 
 
Annika Niedner-Boblenz, Thomas Monecke, Janosch Hennig, Melina Klostermann, Mario Hofweber ...
 
 
 
Adaptive immunity of type VI CRISPR-Cas systems associated with reverse transcriptase'Cas1 fusion proteins border= 
 
María Dolores Molina-Sánchez, Francisco Martínez-Abarca, Vicenta Millán, Mario Rodríguez Mestre, Pavlo Stehantsev ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
Efficient suppression of premature termination codons with alanine by engineered chimeric pyrrolysine tRNAs border= 
 
Aya Awawdeh, Alejandro Tapia, Sarah A Alshawi, Olabode Dawodu, Sarah A Gaier ...
 
 
 
Optogenetic control of Corynebacterium glutamicum gene expression border=  
 
Chen Deng, Ruijie Xin, Xingjian Li, Jie Zhang, Liqiang Fan ...
 
 
 
Correction
 
 
 
 
Correction to ˜Genome manipulation by guide-directed Argonaute cleavage' border= 
 
 
 
 
Correction to ˜Regulation of the androgen receptor by SET9-mediated methylation' border= 
 
 
 
 
Correction to ˜Click display: a rapid and efficient in vitro protein display method for directed evolution' border= 
 
 
 
 
Methods
 
 
 
 
Deep learning insights into distinct patterns of polygenic adaptation across human populations border= 
 
Devashish Tripathi, Chandrika Bhattacharyya, Analabha Basu
 
 
 
A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins border= 
 
Tobias Stadelmann, Daniel Heid, Michael Jendrusch, Jan Mathony, Sabine Aschenbrenner ...
 
 
 
RADIP technology comprehensively identifies H3K27me3-associated RNA'chromatin interactions border= 
 
Xufeng Shu, Masaki Kato, Satoshi Takizawa, Yutaka Suzuki, Piero Carninci
 
 
 
High-throughput capture of transcription factor-driven epigenome dynamics using PHILO ChIP-seq border= 
 
Aanchal Choudhary, Moonia Ammari, Hyuk Sung Yoon, Mark Zander
 
 
 
Utilizing insights of DNA repair machinery to discover MMEJ deletions and novel mechanisms border= 
 
Aditee Kadam, Shay Shilo, Hadas Naor, Alexander Wainstein, Yardena Brilon ...
 
 
 
Simultaneous determination of cytosolic aminoacyl-tRNA synthetase activities by LC'MS/MS border= 
 
Marisa I Mendes, Nicole I Wolf, Joëlle Rudinger-Thirion, Dominic Lenz, Magali Frugier ...
 
 
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