Subject: Nucleic Acids Research Table of Contents for 27 November 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 21
 
27 November 2024
 
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NAR Breakthrough Article
 
 
 
 
STK19 is a transcription-coupled repair factor that participates in UVSSA ubiquitination and TFIIH loading border= 
 
Yuanqing Tan, Meng Gao, Yanchao Huang, Delin Zhan, Sizhong Wu ...
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
Differential redox sensitivity of tRNA dihydrouridylation border= 
 
Lea-Marie Kilz, Simone Zimmermann, Virginie Marchand, Valérie Bourguignon, Claudia Sudol ...
 
 
 
Computational Biology
 
 
 
 
Towards the genomic sequence code of DNA fragility for machine learning border= 
 
Patrick Pflughaupt, Adib A Abdullah, Kairi Masuda, Aleksandr B Sahakyan
 
 
 
Deep learning revealed the distribution and evolution patterns for invertible promoters across bacterial lineages border= 
 
Jiejie Wen, Haobo Zhang, Dongliang Chu, Xiaoke Chen, Jingru Feng ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
ZNF512B binds RBBP4 via a variant NuRD interaction motif and aggregates chromatin in a NuRD complex-independent manner border= 
 
Tim Marius Wunderlich, Chandrika Deshpande, Lena W Paasche, Tobias Friedrich, Felix Diegmüller ...
 
 
 
 
The first chicken oocyte nucleus whole transcriptomic profile defines the spectrum of maternal mRNA and non-coding RNA genes transcribed by the lampbrush chromosomes border= 
 
Alla Krasikova, Tatiana Kulikova, Mikhail Schelkunov, Nadezhda Makarova, Anna Fedotova ...
 
 
 
YY1 is a transcriptional activator of the mouse LINE-1 Tf subfamily border=  
 
Karabi Saha, Grace I Nielsen, Raj Nandani, Yizi Zhang, Lingqi Kong ...
 
 
 
Recruitment of homodimeric proneural factors by conserved CAT'CAT E-boxes drives major epigenetic reconfiguration in cortical neurogenesis border= 
 
Xabier de Martin, Baldomero Oliva, Gabriel Santpere
 
 
 
PWOs repress gene transcription by regulating chromatin structures in Arabidopsis border= 
 
Tingting Yang, Dingyue Wang, Lingxiao Luo, Xiaochang Yin, Zhihan Song ...
 
 
 
A bacterial transcription activator dedicated to the expression of the enzyme catalyzing the first committed step in fatty acid biosynthesis border= 
 
Yuanyou Xu, Zihan Lin, Jiyuan Hou, Kai Ye, Sirui Han ...
 
 
 
 
NusG-dependent RNA polymerase pausing is a common feature of riboswitch regulatory mechanisms border= 
 
Oshadhi T Jayasinghe, Laura E Ritchey, Thomas Breil, Paxton Newman, Helen Yakhnin ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
RAD52-mediated repair of DNA double-stranded breaks at inactive centromeres leads to subsequent apoptotic cell death border= 
 
Gen Maruta, Hisanori Maeoka, Toshiyuki Tsunoda, Kozaburo Akiyoshi, Satoshi Takagi ...
 
 
 
Various plasmid strategies limit the effect of bacterial restriction'modification systems against conjugation border= 
 
Tatiana Dimitriu, Mark D Szczelkun, Edze R Westra
 
 
 
Pathogen-encoded Rum DNA polymerase drives rapid bacterial drug resistance border=  
 
Malgorzata M Jaszczur, Phuong Pham, Debika Ojha, Cecilia Q Pham, John P McDonald ...
 
 
 
SNF2L suppresses nascent DNA gap formation to promote DNA synthesis border=  
 
Anthony Nelligan, Huzefa Dungrawala
 
 
 
PCNA-binding activity separates RNF168 functions in DNA replication and DNA double-stranded break signaling border= 
 
Yang Yang, Deepika Jayaprakash, Satpal S Jhujh, John J Reynolds, Steve Chen ...
 
 
 
Tetrameric INTS6-SOSS1 complex facilitates DNA:RNA hybrid autoregulation at double-strand breaks border= 
 
Qilin Long, Kamal Ajit, Katerina Sedova, Vojtech Haluza, Richard Stefl ...
 
 
 
EGFR-mediated HSP70 phosphorylation facilitates PCNA association with chromatin and DNA replication border= 
 
Yingying Wang, Anthony Fernandez, Xinyu Pei, Bing Liu, Lei Shen ...
 
 
 
Genomics
 
 
 
 
Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome border= 
 
Lari Pyöriä, Diogo Pratas, Mari Toppinen, Peter Simmonds, Klaus Hedman ...
 
 
 
Unveiling host'parasite relationships through conserved MITEs in prokaryote and viral genomes border= 
 
Francisco Nadal-Molero, Riccardo Rosselli, Silvia Garcia-Juan, Alicia Campos-Lopez, Ana-Belen Martin-Cuadrado
 
 
 
Global coupling of R-loop dynamics with RNA polymerase II modulates gene expression and early development of Drosophila border= 
 
Xianhong Zhang, Shao-Bo Liang, Zhuoyun Yi, Zhaohui Qiao, Bo Xu ...
 
 
 
Insertion sequence elements and unique symmetrical genomic regions mediate chromosomal inversions in Streptococcus pyogenes border= 
 
Magnus G Jespersen, Andrew J Hayes, Steven Y C Tong, Mark R Davies
 
 
 
Molecular and Structural Biology
 
 
 
 
A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain border= 
 
Morgan A Esler, Christopher A Belica, Joseph A Rollie, William L Brown, Seyed Arad Moghadasi ...
 
 
 
Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations border= 
 
Yoshita Srivastava, Olayinka Akinyemi, Tiana C Rohe, Elizabeth M Pritchett, Cameron D Baker ...
 
 
 
Coronavirus S protein alters dsRNA accumulation and stress granule formation through regulation of ADAR1-p150 expression border= 
 
Baochao Fan, Yupeng Li, Yi Wang, Shanshan Yang, Qi Peng ...
 
 
 
Structural basis of transcriptional regulation by UrtR in response to uric acid border= 
 
Wan Seok Song, Dong Uk Ki, Hye Yeon Cho, Oh Hyun Kwon, Hongbaek Cho ...
 
 
 
GTSF1 is required for transposon silencing in the unicellular eukaryote Paramecium tetraurelia border= 
 
Chundi Wang, Liping Lyv, Therese Solberg, Haoyue Zhang, Zhiwei Wen ...
 
 
 
RNA G-quadruplex formation in biologically important transcribed regions: can two-tetrad intramolecular RNA quadruplexes be formed? border= 
 
Pritha Basu, Iva Kejnovská, Martin Gajarský, Denis Å ubert, Tereza MikeÅ¡ová ...
 
 
 
Stacking correlation length in single-stranded DNA border=  
 
Xavier Viader-Godoy, Maria Manosas, Felix Ritort
 
 
 
DNA supercoiling enhances DNA condensation by ParB proteins border=  
 
Alejandro Martin-Gonzalez, MiloÅ¡ TiÅ¡ma, Brian T Analikwu, Anders Barth, Richard Janissen ...
 
 
 
ALS-associated FUS mutation reshapes the RNA and protein composition of stress granules border= 
 
Davide Mariani, Adriano Setti, Francesco Castagnetti, Erika Vitiello, Lorenzo Stufera Mecarelli ...
 
 
 
Uncoupling FRUITFULL's functions through modification of a protein motif identified by co-ortholog analysis border= 
 
Kai Thoris, Miguel Correa Marrero, Martijn Fiers, Xuelei Lai, Iris E Zahn ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
A genomic database furnishes minimal functional glycyl-tRNA synthetases homologous to other, designed class II urzymes border= 
 
Sourav Kumar Patra, Jordan Douglas, Peter R Wills, Laurie Betts, Tang Guo Qing ...
 
 
 
RNA and RNA-protein complexes
 
 
 
 
Modulation of UPF1 catalytic activity upon interaction of SARS-CoV-2 Nucleocapsid protein with factors involved in nonsense mediated-mRNA decay border= 
 
Megha Mallick, Volker Boehm, Guangpu Xue, Mark Blackstone, Niels H Gehring ...
 
 
 
Optimized periphery-core interface increases fitness of the Bacillus subtilis glmS ribozyme border= 
 
Li-Eng D Yu, Elise N White, Sarah A Woodson
 
 
 
Taurine hypomodification underlies mitochondrial tRNATrp -related genetic diseases border= 
 
Jia-Li Lu, Yichen Dai, Kunqian Ji, Gui-Xin Peng, Hong Li ...
 
 
 
Human selenocysteine synthase, SEPSECS, has evolved to optimize binding of a tRNA-based substrate border= 
 
Anupama K Puppala, Dylan Sosa, Jennifer Castillo Suchkou, Rachel L French, Malgorzata Dobosz-Bartoszek ...
 
 
 
RNase W, a conserved ribonuclease family with a novel active site border=  
 
Marlène Vayssières, Michael Jüttner, Karina Haas, Aurélie Ancelin, Anita Marchfelder ...
 
 
 
Systematic analysis of the target recognition and repression by the Pumilio proteins border= 
 
Svetlana Farberov, Igor Ulitsky
 
 
 
Alternative substrate kinetics of SARS-CoV-2 Nsp15 endonuclease reveals a specificity landscape dominated by RNA structure border= 
 
Nidhi Kalia, Kimberly C Snell, Michael E Harris
 
 
 
Structural Biology
 
 
 
 
Structural insights into human ELAC2 as a tRNA 3² processing enzyme border= 
 
Chenyang Xue, Junshan Tian, Yanhong Chen, Zhongmin Liu
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity border= 
 
Zhaohong Li, Yuanyuan Zhang, Bo Peng, Shenghua Qin, Qian Zhang ...
 
 
 
Synthetic translational coupling element for multiplexed signal processing and cellular control border= 
 
Hyunseop Goh, Seungdo Choi, Jongmin Kim
 
 
 
Correction
 
 
 
 
Correction to ˜Solution structures and effects of a platinum compound successively bound MYC G-quadruplex' border= 
 
 
 
 
Methods
 
 
 
 
MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylated regions from whole-genome datasets border= 
 
Delphine Balaramane, Yannick G Spill, Michaël Weber, Anaïs Flore Bardet
 
 
 
OmicsFootPrint: a framework to integrate and interpret multi-omics data using circular images and deep neural networks border= 
 
Xiaojia Tang, Naresh Prodduturi, Kevin J Thompson, Richard Weinshilboum, Ciara C O'Sullivan ...
 
 
 
Aptamer-based assay for high-throughput substrate profiling of RNA decapping enzymes border= 
 
Katarzyna Grab, Mateusz Fido, Tomasz Spiewla, Marcin Warminski, Jacek Jemielity ...
 
 
 
Spatial pattern and differential expression analysis with spatial transcriptomic data border= 
 
Fei Qin, Xizhi Luo, Qing Lu, Bo Cai, Feifei Xiao ...
 
 
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