Subject: Nucleic Acids Research Table of Contents for 13 January 2025 Oxford Academic
 
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New issue alert
 
 
 
 
Nucleic Acids Research  
Volume 53 Issue 1
 
13 January 2025
 
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NAR Breakthrough Article
 
 
 
 
The PIWI-interacting protein Gtsf1 controls the selective degradation of small RNAs in Paramecium border= 
 
Olivia Charmant, Julita Gruchota, Olivier Arnaiz, Katarzyna P Nowak, Nicolas Moisan ...
 
 
 
Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure ' Part I: Mg2+ border= 
 
Filip Leonarski, Anja Henning-Knechtel, Serdal Kirmizialtin, Eric Ennifar, Pascal Auffinger
 
 
 
Structural and bioinformatics analyses identify deoxydinucleotide-specific nucleases and their association with genomic islands in gram-positive bacteria border= 
 
Sofia Mortensen, Stanislava Kuncová, Justin D Lormand, Tanner M Myers, Soo-Kyoung Kim ...
 
 
 
Enhanced RNAi does not provide efficient innate antiviral immunity in mice border=  
 
Marcos Iuri Roos Kulmann, Eliska Taborska, Brigita Benköova, Martin Palus, Ales Drobek ...
 
 
 
The role of ribosomal protein networks in ribosome dynamics border=  
 
Youri Timsit, Grégoire Sergeant-Perthuis, Daniel Bennequin
 
 
 
 
 
Critical Reviews and Perspectives
 
 
 
 
Navigating triplet repeats sequencing: concepts, methodological challenges and perspective for Huntington's disease border= 
 
Simone Maestri, Davide Scalzo, Gianluca Damaggio, Martina Zobel, Dario Besusso ...
 
 
 
Translation of circular RNAs border=  
 
Giorgi Margvelani, Karol Andrea Arizaca Maquera, Justin Ralph Welden, David W Rodgers, Stefan Stamm
 
 
 
When repetita no-longer iuvant: somatic instability of the CAG triplet in Huntington's disease border= 
 
Elena Cattaneo, Davide Scalzo, Martina Zobel, Raffaele Iennaco, Camilla Maffezzini ...
 
 
 
Investigating the origins of the mutational signatures in cancer border=  
 
Gunnar Boysen, Ludmil B Alexandrov, Raheleh Rahbari, Intawat Nookaew, Dave Ussery ...
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
Experimental and computational investigations of RNA duplexes containing N7-regioisomers of adenosine and LNA-adenosine border= 
 
Ilyas Yildirim, Witold Andralojc, Amirhossein Taghavi, Daniel Baranowski, Zofia Gdaniec ...
 
 
 
 
A subcellular selective APEX2-based proximity labeling used for identifying mitochondrial G-quadruplex DNA binding proteins border= 
 
Xu Wang, Geng Qin, Jie Yang, Chuanqi Zhao, Jinsong Ren ...
 
 
 
Design and in vitro anticancer assessment of a click chemistry-derived dinuclear copper artificial metallo-nuclease border= 
 
Simon Poole, Obed Akwasi Aning, Vickie McKee, Thomas Catley, Aaraby Yoheswaran Nielsen ...
 
 
 
Unveiling the unusual i-motif-derived architecture of a DNA aptamer exhibiting high affinity for influenza A virus border= 
 
Vladimir Tsvetkov, Bartomeu Mir, Rugiya Alieva, Alexander Arutyunyan, Ilya Oleynikov ...
 
 
 
One-pot ligation of multiple mRNA fragments on dsDNA splint advancing regional modification and translation border= 
 
Yunfan Xu, Shuopeng Qi, Gongrui Zhang, Dan Liu, Dejin Xu ...
 
 
 
Computational Biology
 
 
 
 
Motif distribution in genomes gives insights into gene clustering and co-regulation border= 
 
Atreyi Chakraborty, Sumant Chopde, Mallur Srivatsan Madhusudhan
 
 
 
CICADA: a circRNA effort toward the ghost proteome border=  
 
Liyuan Fan, Xinyuan Zhou, Mian Li, Anwei Gao, Haojie Yu ...
 
 
 
Discovery of highly active kynureninases for cancer immunotherapy through protein language model border= 
 
Hyunuk Eom, Sukhwan Park, Kye Soo Cho, Jihyeon Lee, Hyunbin Kim ...
 
 
 
Selecting genes for analysis using historically contingent progress: from RNA changes to protein'protein interactions border= 
 
Farhaan Lalit, Antony M Jose
 
 
 
Benchmarking cross-species single-cell RNA-seq data integration methods: towards a cell type tree of life border= 
 
Huawen Zhong, Wenkai Han, David Gomez-Cabrero, Jesper Tegner, Xin Gao ...
 
 
 
Data Resources and Analyses
 
 
 
 
Broad repression of DNA repair genes in senescent cells identified by integration of transcriptomic data border= 
 
Yann Frey, Majd Haj, Yael Ziv, Ran Elkon, Yosef Shiloh
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
ATAC and SAGA histone acetyltransferase modules facilitate transcription factor binding to nucleosomes independent of their acetylation activity border= 
 
Kristin V Chesnutt, Gizem Yayli, Christine Toelzer, Mylène Damilot, Khan Cox ...
 
 
 
An sRNA overexpression library reveals AbnZ as a negative regulator of an essential translocation module in Caulobacter crescentus border= 
 
Manuel Velasco-Gomariz, Johannes Sulzer, Franziska Faber, Kathrin S Fröhlich
 
 
 
Piwi regulates the usage of alternative transcription start sites in the Drosophila ovary border= 
 
Jiaying Chen, Na Liu, Hongying Qi, Nils Neuenkirchen, Yuedong Huang ...
 
 
 
Repeated fasting events sensitize enhancers, transcription factor activity and gene expression to support augmented ketogenesis border= 
 
Noga Korenfeld, Meital Charni-Natan, Justine Bruse, Dana Goldberg, Dorin Marciano-Anaki ...
 
 
 
High hydrostatic pressure promotes gene transcription via a cystathionine-beta -synthase domain-containing protein in the hyperthermophilic archaeon Pyrococcus yayanosii border= 
 
Cong Li, Siyuan Li, Qinghao Song, Lin-tai Da, Jun Xu
 
 
 
Molecular mechanisms underlying allosteric behavior of Escherichia coli DgoR, a GntR/FadR family transcriptional regulator border= 
 
Swati Singh, Garima Arya, Rajesh Mishra, Shivam Singla, Akhil Pratap ...
 
 
 
Pervasive RNA-binding protein enrichment on TAD boundaries regulates TAD organization border= 
 
Qiang Sun, Qin Zhou, Yulong Qiao, Xiaona Chen, Hao Sun ...
 
 
 
Single-molecule analysis reveals that IPMK enhances the DNA-binding activity of the transcription factor SRF border= 
 
Hyoungjoon Ahn, Jeongmin Yu, Kwangmin Ryu, Jaeseung Ryu, Sera Kim ...
 
 
 
Cu2+ mediates the oxidation of the transcription factor MscA to regulate the antioxidant defense of mycobacteria border= 
 
Yuling Xiang, Jiachen Zheng, Zhendong Liu, Xujie Cui, Yunfan Zhang ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
Deciphering repair pathways of clustered DNA damage in human TK6 cells: insights from atomic force microscopy direct visualization border= 
 
Toshiaki Nakano, Ken Akamatsu, Masaoki Kohzaki, Masataka Tsuda, Ryoichi Hirayama ...
 
 
 
Comprehensive whole-genome sequencing reveals origins of mutational signatures associated with aging, mismatch repair deficiency and temozolomide chemotherapy border= 
 
Taejoo Hwang, Lukasz Karol Sitko, Ratih Khoirunnisa, Fernanda Navarro-Aguad, David M Samuel ...
 
 
 
RPA and Rad27 limit templated and inverted insertions at DNA breaks border=  
 
Yang Yu, Xin Wang, Jordan Fox, Qian Li, Yang Yu ...
 
 
 
Cell cycle progression of under-replicated cells border=  
 
Min Huang, Chang Yang, Litong Nie, Huimin Zhang, Dandan Zhu ...
 
 
 
Genomics
 
 
 
 
Point mutations in functionally diverse genes are associated with increased natural DNA transformation in multidrug resistant Streptococcus pneumoniae border= 
 
Flora Peillard-Fiorente, Nguyen Phuong Pham, Hélène Gingras, Chantal Godin, Jie Feng ...
 
 
 
Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements border= 
 
Florian Tesson, Erin Huiting, Linlin Wei, Jie Ren, Matthew Johnson ...
 
 
 
Highly accurate Korean draft genomes reveal structural variation highlighting human telomere evolution border= 
 
Jun Kim, Jong Lyul Park, Jin Ok Yang, Sangok Kim, Soobok Joe ...
 
 
 
Molecular and Structural Biology
 
 
 
 
The C-terminal PHDV C5HCH tandem domain of NSD2 is a combinatorial reader of unmodified H3K4 and tri-methylated H3K27 that regulates transcription of cell adhesion genes in multiple myeloma border= 
 
Andrea Berardi, Charlotte Leonie Kaestner, Michela Ghitti, Giacomo Quilici, Paolo Cocomazzi ...
 
 
 
Structural and kinetic insights into tRNA promoter engagement by yeast general transcription factor TFIIIC border= 
 
Wolfram Seifert-Dávila, Anastasiia Chaban, Florence Baudin, Mathias Girbig, Luis Hauptmann ...
 
 
 
Isoleucine-to-valine substitutions support cellular physiology during isoleucine deprivation border= 
 
Gautam Kok, Imre F Schene, Eveline F Ilcken, Paula Sobrevals Alcaraz, Marisa I Mendes ...
 
 
 
Interplay between the Xer recombination system and the dissemination of antibioresistance in Acinetobacter baumannii border= 
 
Corentin Blanchais, Carine Pages, Manuel Campos, Kenza Boubekeur, Rachel Contarin ...
 
 
 
Molecular Biology
 
 
 
 
Force-induced melting and S-DNA pathways for DNA overstretching exhibit distinct kinetics border= 
 
Vinoth Sundar Rajan, Sune Levin, Micah J McCauley, Mark C Williams, Ioulia Rouzina ...
 
 
 
Mechanistic insights into Sindbis virus infection: noncapped genomic RNAs enhance the translation of capped genomic RNAs to promote viral infectivity border= 
 
Deepa Karki, Autumn T LaPointe, Cierra Isom, Milton Thomas, Kevin J Sokoloski
 
 
 
PerR functions as a redox-sensing transcription factor regulating metal homeostasis in the thermoacidophilic archaeon Saccharolobus islandicus REY15A border= 
 
Xuemei Zhang, Pengju Wu, Ruining Bai, Qi Gan, Yunfeng Yang ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
Single-molecule studies reveal the off-pathway early paused state intermediates as a target of streptolydigin inhibition of RNA polymerase and its dramatic enhancement by Gre factors border= 
 
Anatolii Arseniev, Mikhail Panfilov, Georgii Pobegalov, Alina Potyseva, Polina Pavlinova ...
 
 
 
Structural insights into a DNA polymerase reading the xeno nucleic acid HNA border=  
 
Cédric Gutfreund, Karin Betz, Mikhail Abramov, Frédérick Coosemans, Phillipp Holliger ...
 
 
 
Structural basis of Cas9 DNA interrogation with a 5² truncated sgRNA border=  
 
Kaitlyn A Kiernan, Jieun Kwon, Bradley J Merrill, Miljan Simonović
 
 
 
Divergent evolution of opposite base specificity and single-stranded DNA activity in animal and plant AP endonucleases border= 
 
Marina Jordano-Raya, Carol E Schrader, Rafael R Ariza, Teresa Roldán-Arjona, Dolores Córdoba-Cañero
 
 
 
Nucleic Acid Therapeutics
 
 
 
 
Use of a small molecule microarray screen to identify inhibitors of the catalytic RNA subunit of Methanobrevibacter smithii RNase P border= 
 
Vaishnavi Sidharthan, Christopher D Sibley, Kara Dunne-Dombrink, Mo Yang, Walter J Zahurancik ...
 
 
 
High resistance barrier and prophylactic protection in preclinical models of SARS-CoV-2 with two siRNA combination border= 
 
Yesseinia I Anglero-Rodriguez, Florian A Lempp, Megha Subramanian, James McIninch, Mark K Schlegel ...
 
 
 
Direct delivery of Cas-embedded cytosine base editors as ribonucleoprotein complexes for efficient and accurate editing of clinically relevant targets border= 
 
Jeong Min Lee, Jing Zeng, Pengpeng Liu, My Anh Nguyen, Diego Suchenski Loustaunau ...
 
 
 
RNA and RNA-protein complexes
 
 
 
 
Mechanism of activation of contact-dependent growth inhibition tRNase toxin by the amino acid biogenesis factor CysK in the bacterial competition system border= 
 
Zhaohang Feng, Yuka Yashiro, Kozo Tomita
 
 
 
CRISPR-based dissection of miRNA binding sites using isogenic cell lines is hampered by pervasive noise 
 
Mahendra K Prajapat, Andrea G Maria, Joana A Vidigal
 
 
 
Programming ADAR-recruiting hairpin RNA sensor to detect endogenous molecules border= 
 
Pei-Pei Qin, Pin-Ru Chen, Liu Tan, Xiaohe Chu, Bang-Ce Ye ...
 
 
 
Deciphering ligand and metal ion dependent intricate folding landscape of Vc2 c-di-GMP riboswitch aptamer border= 
 
Ji-Yeon Shin, Seo-Ree Choi, So Young An, Kyeong-Mi Bang, Hyun Kyu Song ...
 
 
 
tRNA thiolation optimizes appressorium-mediated infection by enhancing codon-specific translation in Magnaporthe oryzae border= 
 
Xinrong Zhang, Rongrong He, Yinan Li, Shuchao Ren, Shikun Xiang ...
 
 
 
Structural Biology
 
 
 
 
Enzymatic bypass of G-quadruplex structures containing oxidative lesions border= 
 
Peter Podbevšek, Janez Plavec
 
 
 
Visualizing the modification landscape of the human 60S ribosomal subunit at close to atomic resolution border= 
 
Franziska Wiechert, Anett Unbehaun, Thiemo Sprink, Helena Seibel, Jörg Bürger ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
Tuning and functionalization of logic gates for time resolved programming of bacterial populations border= 
 
Leonard E Bäcker, Kevin Broux, Louise Weckx, Sadhana Khanal, Abram Aertsen
 
 
 
Instruction-responsive programmable assemblies with DNA origami block pieces border=  
 
Fang Wang, Xiaolong Shi, Xin Chen, Di Deng, Sirui Li ...
 
 
 
Quadruplet codon decoding-based versatile genetic biocontainment system border=  
 
Yun-Nam Choi, Donghyeon Kim, Seongbeom Lee, Ye Rim Shin, Jeong Wook Lee
 
 
 
Defining serine tRNA knockout as a strategy for effective repression of gene expression in organisms with a recoded genome border= 
 
Peter J Voorhees, Xinyou Chang, Samuel K Lai
 
 
 
CRISPR/Cas13X-assisted programmable and multiplexed translation regulation for controlled biosynthesis border= 
 
Xianhao Xu, Xueqin Lv, Yanfeng Liu, Jianghua Li, Guocheng Du ...
 
 
 
Methods
 
 
 
 
Enhancing disease risk gene discovery by integrating transcription factor-linked trans-variants into transcriptome-wide association analyses border= 
 
Jingni He, Deshan Perera, Wanqing Wen, Jie Ping, Qing Li ...
 
 
 
Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq border= 
 
Delaney K Sullivan, Kristján Eldjárn Hjörleifsson, Nikhila P Swarna, Conrad Oakes, Guillaume Holley ...
 
 
 
QClus: a droplet filtering algorithm for enhanced snRNA-seq data quality in challenging samples border= 
 
Eloi Schmauch, Johannes Ojanen, Kyriakitsa Galani, Juho Jalkanen, Kristiina Harju ...
 
 
 
Detecting a wide range of epitranscriptomic modifications using a nanopore-sequencing-based computational approach with 1D score-clustering border= 
 
Ivan Vujaklija, SiniÅ¡a BiÄ'in, Marin Volarić, Sara Bakić, Zhe Li ...
 
 
 
Corrections
 
 
 
 
Correction to ˜Characterization of an interplay between a Mycobacterium‰tuberculosis MazF homolog, Rv1495 and its sole DNA topoisomerase I' border= 
 
 
 
 
Correction to ˜Enhancing disease risk gene discovery by integrating transcription factor-linked trans-variants into transcriptome-wide association analyses' border= 
 
 
 
 
Correction to "Growth-regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes" border= 
 
 
 
 
Correction to ˜Circular oligomeric particles formed by Ros/MucR family members mediate DNA organization in alpha -proteobacteria' border= 
 
 
 
 
Correction to ˜The Pfam protein families database: embracing AI/ML' border= 
 
 
 
 
Correction to ˜ADAR3 modulates neuronal differentiation and regulates mRNA stability and translation' border= 
 
 
 
 
Correction to ˜AlPaCas: allele-specific CRISPR gene editing through a protospacer-adjacent-motif (PAM) approach' border= 
 
 
 
 
Correction to ˜The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis' border= 
 
 
 
 
Correction to ˜Accelerated discovery and miniaturization of novel single-stranded cytidine deaminases' border= 
 
 
 
 
Correction to ˜GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome' border=  
 
 
 
 
Editor's Note
 
 
 
 
Editor's Note ˜Transcription factor binding sites in the pol geneintragenic regulatory region of HIV-1 are important for virus infectivity' border= 
 
 
 
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