Subject: Nucleic Acids Research Table of Contents for 9 February 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 3
 
9 February 2024
 
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NAR Breakthrough Article
 
 
 
 
Reappraisal of the DNA phosphorothioate modification machinery: uncovering neglected functional modalities and identification of new counter-invader defense systems border= 
 
Siuli Rakesh, L Aravind, Arunkumar Krishnan
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
Minimization of the E. coli ribosome, aided and optimized by community science border= 
 
Tiyaporn Tangpradabkul, Michael Palo, Jill Townley, Kenneth B Hsu, Eterna participants ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
Post-transcriptional regulation shapes the transcriptome of quiescent budding yeast border= 
 
Alison C Greenlaw, Kris G Alavattam, Toshio Tsukiyama
 
 
 
Functional analysis of the AUG initiator codon context reveals novel conserved sequences that disfavor mRNA translation in eukaryotes border= 
 
Greco Hernández, Alejandra García, Shira Weingarten-Gabbay, Rishi Kumar Mishra, Tanweer Hussain ...
 
 
 
A tailed mirtron promotes longevity in Drosophila border=  
 
Sweta Khanal, Matthew de Cruz, Britton Strickland, Kody Mansfield, Eric C Lai ...
 
 
 
 
Exonic splicing code and coordination of divalent metals in proteins border= 
 
Dara Bakhtiar, Katarina Vondraskova, Reuben J Pengelly, Martin Chivers, Jana Kralovicova ...
 
 
 
Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression border= 
 
Martin Loza, Alexis Vandenbon, Kenta Nakai
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
MutSbeta protects common fragile sites by facilitating homology-directed repair at DNA double-strand breaks with secondary structures border= 
 
Youhang Li, Yunkun Zhang, Sameer Bikram Shah, Chia-Yu Chang, Hailong Wang ...
 
 
 
DAXX promotes centromeric stability independently of ATRX by preventing the accumulation of R-loop-induced DNA double-stranded breaks border= 
 
Lia M Pinto, Alexandros Pailas, Max Bondarchenko, Abhishek Bharadwaj Sharma, Katrin Neumann ...
 
 
 
Spatial regulation of DNA damage tolerance protein Rad5 interconnects genome stability maintenance and proteostasis networks border= 
 
Carl P Lehmann, Paula González-Fernández, José Antonio Tercero
 
 
 
 
The protein phosphatase EYA4 promotes homologous recombination (HR) through dephosphorylation of tyrosine 315 on RAD51 border= 
 
Bárbara de la Peña Avalos, Nicolas Paquet, Romain Tropée, Yan Coulombe, Hannah Palacios ...
 
 
 
cGAS-STING signalling regulates microglial chemotaxis in genome instability border=  
 
Emily J Talbot, Lisha Joshi, Peter Thornton, Mahya Dezfouli, Kalliopi Tsafou ...
 
 
 
Genomics
 
 
 
 
Light-strand bias and enriched zones of embedded ribonucleotides are associated with DNA replication and transcription in the human-mitochondrial genome border= 
 
Penghao Xu, Taehwan Yang, Deepali L Kundnani, Mo Sun, Stefania Marsili ...
 
 
 
Recent reactivation of a pathogenicity-associated transposable element is associated with major chromosomal rearrangements in a fungal wheat pathogen border= 
 
Thomas Badet, Sabina Moser Tralamazza, Alice Feurtey, Daniel Croll
 
 
 
The roles of DNA methylation on pH dependent i-motif (iM) formation in rice border= 
 
Yilong Feng, Xing Ma, Ying Yang, Shentong Tao, Asgar Ahmed ...
 
 
 
Molecular Biology
 
 
 
 
Alternative cleavage and polyadenylation of the Ccnb1 mRNA defines accumulation of cyclin protein during the meiotic cell cycle border= 
 
Xiaotian Wang, Fang-Shiuan Leung, Jeffrey O Bush, Marco Conti
 
 
 
Using transition density models to interpret experimental optical spectra of exciton-coupled cyanine (iCy3)2 dimer probes of local DNA conformations at or near functional protein binding sites border= 
 
Dylan Heussman, Lulu Enkhbaatar, Mohammed I Sorour, Kurt A Kistler, Peter H von Hippel ...
 
 
 
Replication elongates short DNA, reduces sequence bias and develops trimer structure border= 
 
Adriana Calaça Serrão, Felix T Dänekamp, Zsófia Meggyesi, Dieter Braun
 
 
 
A phage-encoded RNA-binding protein inhibits the antiviral activity of a toxin'antitoxin system border= 
 
Chantal K Guegler, Gabriella I C Teodoro, Sriram Srikant, Keerthana Chetlapalli, Christopher R Doering ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
Using energy to go downhill'a genoprotective role for ATPase activity in DNA topoisomerase II border= 
 
Afif F Bandak, Tim R Blower, Karin C Nitiss, Viraj Shah, John L Nitiss ...
 
 
 
An exonuclease-resistant chain-terminating nucleotide analogue targeting the SARS-CoV-2 replicase complex border= 
 
Ashleigh Shannon, Aurélie Chazot, Mikael Feracci, Camille Falcou, Véronique Fattorini ...
 
 
 
Pathological mutations promote proteolysis of mitochondrial tRNA-specific 2-thiouridylase 1 (MTU1) via mitochondrial caseinolytic peptidase (CLPP) border= 
 
Raja Norazireen Raja Ahmad, Long-Teng Zhang, Rikuri Morita, Haruna Tani, Yong Wu ...
 
 
 
RNA and RNA-protein complexes
 
 
 
 
Internal RNA 2²-O -methylation on the HIV-1 genome impairs reverse transcription border= 
 
Alice Decombe, Olve Peersen, Priscila Sutto-Ortiz, Célia Chamontin, Géraldine Piorkowski ...
 
 
 
Contribution of tRNA sequence and modifications to the decoding preferences of E. coli and M. mycoides tRNAGly UCC for synonymous glycine codons border= 
 
Maria Kompatscher, Karolina Bartosik, Kevin Erharter, Raphael Plangger, Fabian Sebastian Juen ...
 
 
 
ESRP1 controls biogenesis and function of a large abundant multiexon circRNA border=  
 
Dawei Liu, B Kate Dredge, Andrew G Bert, Katherine A Pillman, John Toubia ...
 
 
 
The previously uncharacterized RnpM (YlxR) protein modulates the activity of ribonuclease P in Bacillus subtilis in vitro border= 
 
Dennis Wicke, Piotr Neumann, Markus Gößringer, Aleksandar Chernev, Swetlana Davydov ...
 
 
 
Global analysis of binding sites of U2AF1 and ZRSR2 reveals RNA elements required for mutually exclusive splicing by the U2- and U12-type spliceosome border= 
 
Young-Soo Kwon, Sang Woo Jin, Hoseok Song
 
 
 
Structural Biology
 
 
 
 
Structure of the WYL-domain containing transcription activator, DriD, in complex with ssDNA effector and DNA target site border= 
 
Maria A Schumacher, Emily Cannistraci, Raul Salinas, Devin Lloyd, Ella Messner ...
 
 
 
Harmonin homology domain-mediated interaction of RTEL1 helicase with RPA and DNA provides insights into its recruitment to DNA repair sites border= 
 
Niranjan Kumar, Arushi Taneja, Meenakshi Ghosh, Ulli Rothweiler, Nagalingam Ravi Sundaresan ...
 
 
 
Structural basis for transcription activation by the nitrate-responsive regulator NarL border= 
 
Dmytro Kompaniiets, Lina He, Dong Wang, Wei Zhou, Yang Yang ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
Scaffold RNA engineering in type V CRISPR-Cas systems: a potent way to enhance gene expression in the yeast Saccharomyces cerevisiae border= 
 
Lifang Yu, Mario Andrea Marchisio
 
 
 
Rapid human genomic DNA cloning into mouse artificial chromosome via direct chromosome transfer from human iPSC and CRISPR/Cas9-mediated translocation border= 
 
Hitomaru Miyamoto, Hiroaki Kobayashi, Nanami Kishima, Kyotaro Yamazaki, Shusei Hamamichi ...
 
 
 
Enhancing circuit stability under growth feedback with supplementary repressive regulation border= 
 
Austin Stone, Sadikshya Rijal, Rong Zhang, Xiao-Jun Tian
 
 
 
Correction
 
 
 
 
Correction to ˜Srsf1 and Elavl1 act antagonistically on neuronal fate choice in the developing neocortex by controlling TrkC receptor isoform expression' border= 
 
 
 
 
Correction to ˜Effective extraction of polyribosomes exposes gene expression strategies in primary astrocytes' border= 
 
 
 
 
Correction to ˜Using energy to go downhill'a genoprotective role for ATPase activity in DNA topoisomerase II' border= 
 
 
 
 
Methods
 
 
 
 
Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses border= 
 
Samuel Coulbourn Flores, Michal Malý, Dominik Hrebík, Pavel Plevka, JiÅ™í Ä'erný
 
 
 
Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR border= 
 
Pedro L Baldoni, Yunshun Chen, Soroor Hediyeh-zadeh, Yang Liao, Xueyi Dong ...
 
 
 
Differentiable partition function calculation for RNA border=  
 
Marco C Matthies, Ryan Krueger, Andrew E Torda, Max Ward
 
 
 
Pasa: leveraging population pangenome graph to scaffold prokaryote genome assemblies border= 
 
Van Hoan Do, Son Hoang Nguyen, Duc Quang Le, Tam Thi Nguyen, Canh Hao Nguyen ...
 
 
 
HetFCM: functional co-module discovery by heterogeneous network co-clustering border=  
 
Haojiang Tan, Maozu Guo, Jian Chen, Jun Wang, Guoxian Yu
 
 
 
Gene set correlation enrichment analysis for interpreting and annotating gene expression profiles border= 
 
Lan-Yun Chang, Meng-Zhan Lee, Yujia Wu, Wen-Kai Lee, Chia-Liang Ma ...
 
 
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