Subject: Nucleic Acids Research Table of Contents for 21 March 2024 Oxford Academic
 
 
 
Oxford Academic
 
 
 
 
New issue alert
 
 
 
 
Celebrating 50 years of cutting-edge research!
 

Since its inception, Nucleic Acids Research has built its reputation as a leading journal in the molecular and cellular biologicals sciences by publishing high-quality research and promoting the use of information technology in biological research. We want to thank our editors, readers, reviewers, and authors for helping us reach this significant milestone! 

Read the celebratory editorial from NAR Senior Executive Editors, Julian Sale and Barry Stoddard
 
 
 
 
Nucleic Acids Research  
Volume 52 Issue 5
 
21 March 2024
 
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NAR Breakthrough Article
 
 
 
 
Xrp1 governs the stress response program to spliceosome dysfunction border= 
 
Dimitrije Stanković, Luke S Tain, Mirka Uhlirova
 
 
 
Critical Reviews and Perspectives
 
 
 
 
The SMC5/6 complex: folding chromosomes back into shape when genomes take a break border= 
 
Shamayita Roy, Hemanta Adhikary, Damien D'Amours
 
 
 
When Paul Berg meets Donald Crothers: an achiral connection through protein biosynthesis border= 
 
Pradeep Kumar, Rajan Sankaranarayanan
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity border= 
 
Hui-ting Liang, Jiang-yu Yan, Hao-jun Yao, Xue-nan Zhang, Zhi-ming Xing ...
 
 
 
Molecular and thermodynamic determinants of self-assembly and hetero-oligomerization in the enterobacterial thermo-osmo-regulatory protein H-NS border= 
 
Bincy Lukose, Takahiro Maruno, Mohammed A Faidh, Susumu Uchiyama, Athi N Naganathan
 
 
 
 
Transient states during the annealing of mismatched and bulged oligonucleotides border= 
 
Marco Todisco, Dian Ding, Jack W Szostak
 
 
 
Computational Biology
 
 
 
 
Prediction of DNA i-motifs via machine learning border= 
 
Bibo Yang, Dilek Guneri, Haopeng Yu, Elisé P Wright, Wenqian Chen ...
 
 
 
G-quadruplex-mediated genomic instability drives SNVs in cancer border=  
 
Tilmann Richl, Jochen Kuper, Caroline Kisker
 
 
 
Data Resources and Analyses
 
 
 
 
Human pangenome analysis of sequences missing from the reference genome reveals their widespread evolutionary, phenotypic, and functional roles border= 
 
Zhikun Wu, Tong Li, Zehang Jiang, Jingjing Zheng, Yizhou Gu ...
 
 
 
RNAvigate: efficient exploration of RNA chemical probing datasets border=  
 
Patrick S Irving, Kevin M Weeks
 
 
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
Yeast zinc cluster transcription factors involved in the switch from fermentation to respiration show interdependency for DNA binding revealing a novel type of DNA recognition border= 
 
Karla Páez Martinez, Najla Gasmi, Célia Jeronimo, Natalia Klimova, François Robert ...
 
 
 
Intrinsically disordered regions of the Msn2 transcription factor encode multiple functions using interwoven sequence grammars border= 
 
Vladimir Mindel, Sagie Brodsky, Aileen Cohen, Wajd Manadre, Felix Jonas ...
 
 
 
Histone lactylation-boosted ALKBH3 potentiates tumor progression and diminished promyelocytic leukemia protein nuclear condensates by m1 A demethylation of SP100A border= 
 
Xiang Gu, Ai Zhuang, Jie Yu, Ludi Yang, Shengfang Ge ...
 
 
 
G-quadruplexes control hepatitis B virus replication by promoting cccDNA transcription and phase separation in hepatocytes border= 
 
Guillaume Giraud, Mélanie Rodà, Pélagie Huchon, Maud Michelet, Sarah Maadadi ...
 
 
 
PRC1 directs PRC2-H3K27me3 deposition to shield adult spermatogonial stem cells from differentiation border= 
 
Mengwen Hu, Yu-Han Yeh, So Maezawa, Toshinori Nakagawa, Shosei Yoshida ...
 
 
 
Global Hfq-mediated RNA interactome of nitrogen starved Escherichia coli uncovers a conserved post-transcriptional regulatory axis required for optimal growth recovery border= 
 
Josh McQuail, Gianluca Matera, Tom Gräfenhan, Thorsten Bischler, Per Haberkant ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
USP1-dependent nucleolytic expansion of PRIMPOL-generated nascent DNA strand discontinuities during replication stress border= 
 
Alexandra Nusawardhana, Lindsey M Pale, Claudia M Nicolae, George-Lucian Moldovan
 
 
 
Rif2 interaction with Rad50 counteracts Tel1 functions in checkpoint signalling and DNA tethering by releasing Tel1 from MRX binding border= 
 
Paolo Pizzul, Erika Casari, Carlo Rinaldi, Marco Gnugnoli, Marco Mangiagalli ...
 
 
 
Aberrant DNA repair reveals a vulnerability in histone H3.3-mutant brain tumors border= 
 
Giulia Giacomini, Sandra Piquet, Odile Chevallier, Juliette Dabin, Siau-Kun Bai ...
 
 
 
STIM1 translocation to the nucleus protects cells from DNA damage border=  
 
Irene Sanchez-Lopez, Yolanda Orantos-Aguilera, Eulalia Pozo-Guisado, Alberto Alvarez-Barrientos, Sergio Lilla ...
 
 
 
Site-specific acetylation of polynucleotide kinase 3²-phosphatase regulates its distinct role in DNA repair pathways border= 
 
Azharul Islam, Anirban Chakraborty, Altaf H Sarker, Uma K Aryal, Lang Pan ...
 
 
 
Genomics
 
 
 
 
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast border= 
 
Elie M Teyssonniere, Yuichi Shichino, Mari Mito, Anne Friedrich, Shintaro Iwasaki ...
 
 
 
Large-scale duplication events underpin population-level flexibility in tRNA gene copy number in Pseudomonas fluorescens SBW25 border= 
 
Zahra Khomarbaghi, Wing Y Ngan, Gökçe B Ayan, Sungbin Lim, Gunda Dechow-Seligmann ...
 
 
 
Molecular Biology
 
 
 
 
Ribosomal frameshifting at normal codon repeats recodes functional chimeric proteins in human border= 
 
Guiping Ren, Xiaoqian Gu, Lu Zhang, Shimin Gong, Shuang Song ...
 
 
 
The unique dual targeting of AGO1 by two types of PRMT enzymes promotes phasiRNA loading in Arabidopsis thaliana border= 
 
Clément Barre-Villeneuve, Michèle Laudié, Marie-Christine Carpentier, Lauriane Kuhn, Thierry Lagrange ...
 
 
 
Two birds with one stone: SGI1 can stabilize itself and expel the IncC helper by hijacking the plasmid parABS system border= 
 
Gábor Murányi, Mónika Szabó, Károly Acsai, János Kiss
 
 
 
The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations border= 
 
Hai-Long Dong, Chen Zhang, Liang Dai, Yan Zhang, Xing-Hua Zhang ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein border= 
 
Elena Manakova, Edvardas Golovinas, Reda PoceviÄiÅ«tÄ-, Giedrius Sasnauskas, Arunas Silanskas ...
 
 
 
Thiolutin has complex effects in vivo but is a direct inhibitor of RNA polymerase II in vitro border= 
 
Chenxi Qiu, Payal Arora, Indranil Malik, Amber J Laperuta, Emily M Pavlovic ...
 
 
 
Homology recognition without double-stranded DNA-strand separation in D-loop formation by RecA border= 
 
Takehiko Shibata, Shukuko Ikawa, Wakana Iwasaki, Hiroyuki Sasanuma, Hisao Masai ...
 
 
 
Trans-complementation by the RecB nuclease domain of RecBCD enzyme reveals new insight into RecA loading upon χ recognition border= 
 
Theetha L Pavankumar, C Jason Wong, Yun Ka Wong, Maria Spies, Stephen C Kowalczykowski
 
 
 
RNA and RNA-protein complexes
 
 
 
 
piRNA generation is associated with the pioneer round of translation in stem cells border= 
 
Sudheesh Allikka Parambil, Danyan Li, Michael Zelko, Axel Poulet, Josien C van Wolfswinkel
 
 
 
The disordered N-terminal tail of SARS-CoV-2 Nucleocapsid protein forms a dynamic complex with RNA border= 
 
Jasmine Cubuk, Jhullian J Alston, J Jeremías Incicco, Alex S Holehouse, Kathleen B Hall ...
 
 
 
Heterogeneous nuclear ribonucleoprotein K promotes cap-independent translation initiation of retroviral mRNAs border= 
 
Yazmín Fuentes, Valeria Olguín, Brenda López-Ulloa, Dafne Mendonça, Hade Ramos ...
 
 
 
METTL3 drives telomere targeting of TERRA lncRNA through m6 A-dependent R-loop formation: a therapeutic target for ALT-positive neuroblastoma border= 
 
Roshan Vaid, Ketan Thombare, Akram Mendez, Rebeca Burgos-Panadero, Anna Djos ...
 
 
 
Structural Biology
 
 
 
 
NMR measurements of transient low-populated tautomeric and anionic Watson'Crick-like G·T/U in RNA:DNA hybrids: implications for the fidelity of transcription and CRISPR/Cas9 gene editing border= 
 
Or Szekely, Atul Kaushik Rangadurai, Stephanie Gu, Akanksha Manghrani, Serafima Guseva ...
 
 
 
Understanding intercalative modulation of G-rich sequence folding: solution structure of a TINA-conjugated antiparallel DNA triplex border= 
 
Miguel Garavís, Patrick J B Edwards, Israel Serrano-Chacón, Osman Doluca, Vyacheslav V Filichev ...
 
 
 
Structural investigation of pathogenic RFC1 AAGGG pentanucleotide repeats reveals a role of G-quadruplex in dysregulated gene expression in CANVAS border= 
 
Yang Wang, Junyan Wang, Zhenzhen Yan, Jianing Hou, Liqi Wan ...
 
 
 
Structural insights into the HDAC4'MEF2A'DNA complex and its implication in long-range transcriptional regulation border= 
 
Shuyan Dai, Liang Guo, Raja Dey, Ming Guo, Xiangqian Zhang ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
Mage transposon: a novel gene delivery system for mammalian cells border= 
 
Jinghan Tian, Doudou Tong, Zhendong Li, Erqiang Wang, Yifei Yu ...
 
 
 
Selection-free precise gene repair using high-capacity adenovector delivery of advanced prime editing systems rescues dystrophin synthesis in DMD muscle cells border= 
 
Qian Wang, Sabrina Capelletti, Jin Liu, Josephine M Janssen, Manuel A F V Gonçalves
 
 
 
Correction
 
 
 
 
Correction to ˜PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs' border= 
 
 
 
 
Correction to ˜HDGFRP3 interaction with 53BP1 promotes DNA double-strand break repair' border= 
 
 
 
 
Methods
 
 
 
 
Smoother: on-the-fly processing of interactome data using prefix sums border= 
 
Markus R Schmidt, Anna Barcons-Simon, Claudia Rabuffo, T Nicolai Siegel
 
 
 
Uncovering the roles of DNA hemi-methylation in transcriptional regulation using MspJI-assisted hemi-methylation sequencing border= 
 
Xiong Xiong, Hengye Chen, Qifan Zhang, Yangying Liu, Chenhuan Xu
 
 
 
MMCT-Loop: a mix model-based pipeline for calling targeted 3D chromatin loops border=  
 
Li Tang, Jiaqi Liao, Matthew C Hill, Jiaxin Hu, Yichao Zhao ...
 
 
 
SHIFTR enables the unbiased identification of proteins bound to specific RNA regions in live cells border= 
 
Jens Aydin, Alexander Gabel, Sebastian Zielinski, Sabina Ganskih, Nora Schmidt ...
 
 
 
EquiPNAS: improved protein'nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks border= 
 
Rahmatullah Roche, Bernard Moussad, Md Hossain Shuvo, Sumit Tarafder, Debswapna Bhattacharya
 
 
 
Nucleotide-level distance metrics to quantify alternative splicing implemented in TranD border= 
 
Adalena Nanni, James Titus-McQuillan, Kinfeosioluwa S Bankole, Francisco Pardo-Palacios, Sarah Signor ...
 
 
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