Subject: Nucleic Acids Research Table of Contents for 28 October 2024 Oxford Academic
 
 
 
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 19
 
28 October 2024
 
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NAR Breakthrough Article
 
 
 
 
RNA-directed peptide synthesis across a nicked loop border= 
 
Meng Su, Samuel J Roberts, John D Sutherland
 
 
 
Critical Reviews and Perspectives
 
 
 
 
Closing in on human methylation'the versatile family of seven-beta -strand (METTL) methyltransferases border= 
 
Pål Ø Falnes
 
 
 
DNA-binding proteins from MBD through ZF to BEN: recognition of cytosine methylation status by one arginine with two conformations border= 
 
Xing Zhang, Robert M Blumenthal, Xiaodong Cheng
 
 
 
Computational Biology
 
 
 
 
Advancing microRNA target site prediction with transformer and base-pairing patterns border= 
 
Yue Bi, Fuyi Li, Cong Wang, Tong Pan, Chen Davidovich ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
A plant-specific clade of serine/arginine-rich proteins regulates RNA splicing homeostasis and thermotolerance in tomato border= 
 
Remus R E Rosenkranz, Stavros Vraggalas, Mario Keller, Srimeenakshi Sankaranarayanan, François McNicoll ...
 
 
 
 
CRISPR screening uncovers nucleolar RPL22 as a heterochromatin destabilizer and senescence driver border= 
 
Hong-Yu Li, Min Wang, Xiaoyu Jiang, Yaobin Jing, Zeming Wu ...
 
 
 
LAP2alpha facilitates myogenic gene expression by preventing nucleoplasmic lamin A/C from spreading to active chromatin regions border= 
 
Simona Ferraioli, Fatih Sarigol, Celine Prakash, Daria Filipczak, Roland Foisner ...
 
 
 
DNA methylation by CcrM contributes to genome maintenance in the Agrobacterium tumefaciens plant pathogen border= 
 
Sandra Martin, Florian Fournes, Giovanna Ambrosini, Christian Iseli, Karolina Bojkowska ...
 
 
 
Engineered Cas9 variants bypass Keap1-mediated degradation in human cells and enhance epigenome editing efficiency border= 
 
Jianfeng Chen, Siyuan Su, Adrian Pickar-Oliver, Anna M Chiarella, Quentin Hahn ...
 
 
 
A single rare Ïƒ70 variant establishes a unique gene expression pattern in the E. coli pathobiont LF82 
 
Melissa Arroyo-Mendoza, Alexandra Proctor, Abraham Correa-Medina, Sarah DeWolf, Meghan Wymore Brand ...
 
 
 
 
G-quadruplexes in an SVA retrotransposon cause aberrant TAF1 gene expression in X-linked dystonia parkinsonism border= 
 
Giulia Nicoletto, Marianna Terreri, Ilaria Maurizio, Emanuela Ruggiero, Filippo M Cernilogar ...
 
 
 
Chem-CRISPR/dCas9FCPF : a platform for chemically induced epigenome editing border= 
 
Mukaddes Altinbay, Jianhui Wang, Jie Chen, Daniel Schäfer, Maximilian Sprang ...
 
 
 
Transcription start site scanning requires the fungi-specific hydrophobic loop of Tfb3 border= 
 
Chun Yang, Pratik Basnet, Samah Sharmin, Hui Shen, Craig D Kaplan ...
 
 
 
Testis-specific H2B.W1 disrupts nucleosome integrity by reducing DNA'histone interactions border= 
 
Dongbo Ding, Matthew Y H Pang, Mingxi Deng, Thi Thuy Nguyen, Yue Liu ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation border= 
 
Rahul Chadda, Vikas Kaushik, Iram Munir Ahmad, Jaigeeth Deveryshetty, Alex S Holehouse ...
 
 
 
Synergistic action of human RNaseH2 and the RNA helicase-nuclease DDX3X in processing R-loops border= 
 
Massimiliano Secchi, Anna Garbelli, Valentina Riva, Graziano Deidda, Carolina Santonicola ...
 
 
 
Histone variant macroH2A1 regulates synchronous firing of replication origins in the inactive X chromosome border= 
 
Maria Arroyo, Corella S Casas-Delucchi, Maruthi K Pabba, Paulina Prorok, Sunil K Pradhan ...
 
 
 
Elucidation of the molecular mechanism of the breakage-fusion-bridge (BFB) cycle using a CRISPR-dCas9 cellular model border= 
 
Manrose Singh, Kaitlin Raseley, Alexis M Perez, Danny MacKenzie, Settapong T Kosiyatrakul ...
 
 
 
Nucleotide excision repair of aflatoxin-induced DNA damage within the 3D human genome organization border= 
 
Yiran Wu, Muhammad Muzammal Adeel, Dian Xia, Aziz Sancar, Wentao Li
 
 
 
PARP1-TRIM44-MRN loop dictates the response to PARP inhibitors border=  
 
Yonghyeon Kim, Sunwoo Min, Soyeon Kim, Seo Yun Lee, Yeon-Ji Park ...
 
 
 
Mechanism of BCDX2-mediated RAD51 nucleation on short ssDNA stretches and fork DNA border= 
 
Masaki Akita, Paul Girvan, Mario Spirek, Jiri Novacek, David Rueda ...
 
 
 
DNA double-strand break movement in heterochromatin depends on the histone acetyltransferase dGcn5 border= 
 
Apfrida Kendek, Arianna Sandron, Jan-Paul Lambooij, Serafin U Colmenares, Severina M Pociunaite ...
 
 
 
Mei5'Sae3 stabilizes Dmc1 nucleating clusters for efficient Dmc1 assembly on RPA-coated single-stranded DNA border= 
 
Chin-Dian Wei, Hao-Yen Chang, Chia-Hua Lu, Chih-Chun Chang, Asako Furukohri ...
 
 
 
Polyubiquitinated PCNA triggers SLX4-mediated break-induced replication in alternative lengthening of telomeres (ALT) cancer cells border= 
 
Sangin Kim, Su Hyung Park, Nalae Kang, Jae Sun Ra, Kyungjae Myung ...
 
 
 
Molecular and Structural Biology
 
 
 
 
A transcription-independent role for HIF-1alpha in modulating microprocessor assembly border= 
 
Jie-Ning Li, Ming-Yang Wang, Jhen-Wei Ruan, Yu-Jhen Lyu, Yi-Hsiu Weng ...
 
 
 
The transition state for coupled folding and binding of a disordered DNA binding domain resembles the unbound state border= 
 
Mikhail Kuravsky, Conor Kelly, Christina Redfield, Sarah L Shammas
 
 
 
Stochastic nature and physiological implications of 5²-NAD RNA cap in bacteria border= 
 
Jana Wiedermannová, Ravishankar Babu, Yulia Yuzenkova
 
 
 
Phage defence loci of Streptococcus thermophilus' tip of the anti-phage iceberg? border= 
 
Philip Kelleher, Guillermo Ortiz Charneco, Zoe Kampff, Natalia Diaz-Garrido, Francesca Bottacini ...
 
 
 
Kinetic mechanism and determinants of EF-P recruitment to translating ribosomes border= 
 
Vitalii Mudryi, Jan Ole Frister, Bee-Zen Peng, Ingo Wohlgemuth, Frank Peske ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity border= 
 
Tongshan Zuo, Chen Shen, Zhen Xie, Guanhong Xu, Fangdi Wei ...
 
 
 
Structural and mechanistic insights into a mesophilic prokaryotic Argonaute border=  
 
Xin Tao, Hui Ding, Shaowen Wu, Fei Wang, Hu Xu ...
 
 
 
Nucleic Acid Therapeutics
 
 
 
 
Amphiphilic shuttle peptide delivers base editor ribonucleoprotein to correct the CFTR R553X mutation in well-differentiated airway epithelial cells border= 
 
Katarina Kulhankova, Anna X Cheng, Soumba Traore, Maud Auger, Mia Pelletier ...
 
 
 
RNA and RNA-protein complexes
 
 
 
 
A CRISPR-dCas13 RNA-editing tool to study alternative splicing border= 
 
Yaiza Núñez-Álvarez, Tristan Espie-Caullet, Géraldine Buhagiar, Ane Rubio-Zulaika, Josune Alonso-Marañón ...
 
 
 
KREH2 helicase represses ND7 mRNA editing in procyclic-stage Trypanosoma brucei by opposite modulation of canonical and ˜moonlighting' gRNA utilization creating a proposed mRNA structure border= 
 
Joshua Meehan, Alasdair Ivens, Scott Grote, Tyler Rodshagen, Zihao Chen ...
 
 
 
Sarbecovirus programmed ribosome frameshift RNA element folding studied by NMR spectroscopy and comparative analyses border= 
 
María Hernández-Marín, Ángel Cantero-Camacho, Ignacio Mena, Sergio López-Núñez, Adolfo García-Sastre ...
 
 
 
RNA helicase D1PAS1 resolves R-loops and forms a complex for mouse pachytene piRNA biogenesis required for male fertility 
 
Heejin Choi, Lecong Zhou, Yangu Zhao, Jurrien Dean
 
 
 
Elucidating microRNA-34a organisation within human Argonaute-2 by dynamic nuclear polarisation-enhanced magic angle spinning NMR border= 
 
Rubin Dasgupta, Walter Becker, Katja Petzold
 
 
 
The ABCF ATPase New1 resolves translation termination defects associated with specific tRNAArg and tRNALys isoacceptors in the P site border= 
 
Kathryn Turnbull, Helge Paternoga, Esther von der Weth, Artyom A Egorov, Agnieszka A Pochopien ...
 
 
 
ADAR3 modulates neuronal differentiation and regulates mRNA stability and translation border= 
 
Victor Karlström, Eduardo A Sagredo, Jordi Planells, Charlotte Welinder, Jennifer Jungfleisch ...
 
 
 
Eukaryotic initiation factor 4B is a multi-functional RNA binding protein that regulates histone mRNAs border= 
 
Ana Quintas, Robert F Harvey, Emilie Horvilleur, Gavin D Garland, Tobias Schmidt ...
 
 
 
MBNL splicing factors regulate the microtranscriptome of skeletal muscles border=  
 
Agnieszka Piasecka, MichaÅ‚ W SzczeÅ›niak, MichaÅ‚ Sekrecki, Arkadiusz Kajdasz, Å ukasz J Sznajder ...
 
 
 
Combining Nanopore direct RNA sequencing with genetics and mass spectrometry for analysis of T-loop base modifications across 42 yeast tRNA isoacceptors border= 
 
Ethan A Shaw, Niki K Thomas, Joshua D Jones, Robin L Abu-Shumays, Abigail L Vaaler ...
 
 
 
Methods
 
 
 
 
DNA breathing integration with deep learning foundational model advances genome-wide binding prediction of human transcription factors 
 
Anowarul Kabir, Manish Bhattarai, Selma Peterson, Yonatan Najman-Licht, Kim Ø Rasmussen ...
 
 
 
A deep learning-based method enables the automatic and accurate assembly of chromosome-level genomes border= 
 
Zijie Jiang, Zhixiang Peng, Zhaoyuan Wei, Jiahe Sun, Yongjiang Luo ...
 
 
 
IRescue: uncertainty-aware quantification of transposable elements expression at single cell level border= 
 
Benedetto Polimeni, Federica Marasca, Valeria Ranzani, Beatrice Bodega
 
 
 
4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs border= 
 
Lianrong Pu, Ron Shamir
 
 
 
Enhanced Golden Gate Assembly: evaluating overhang strength for improved ligation efficiency border= 
 
Patryk Strzelecki, Nicolas Joly, Pascal Hébraud, Elise Hoffmann, Grzegorz M Cech ...
 
 
 
High-throughput single telomere analysis using DNA microarray and fluorescent in situ hybridization border= 
 
Yun-Ling Zheng, Xingjia Wu, Madeline Williams, Simon Verhulst, Jue Lin ...
 
 
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