Subject: Nucleic Acids Research Table of Contents for 24 April 2024 Oxford Academic
 
 
 
Oxford Academic
 
 
 
 
New issue alert
 
 
 
 
Celebrating 50 years of NAR
 

Nucleic Acids Research is celebrating its 50th anniversary this year. We owe our success to the incredible work of the three founding editors, Richard T. Walker and A. Stanley Jones at the University of Birmingham in the UK, and Dieter Söll at Yale University in the USA. Their vision and dedication have been carried forward by the editors who followed them, as well as our authors and reviewers. Today, NAR remains one of the leading journals in the biological sciences. 

Celebrate our 50th anniversary with us
 
 
 
 
Nucleic Acids Research  
Volume 52 Issue 7
 
24 April 2024
 
button-issue.png
 
 
Editorial
 
 
 
 
CRISPR in Nucleic Acids Research: the sequel border= 
 
Julian E Sale, Barry L Stoddard
 
 
 
Computational Biology
 
 
 
 
Origin, evolution, and maintenance of gene-strand bias in bacteria border= 
 
Malhar Atre, Bharat Joshi, Jebin Babu, Shabduli Sawant, Shreya Sharma ...
 
 
 
Determinant of m6A regional preference by transcriptional dynamics border=  
 
Yalan Wang, Shen Wang, Zhen Meng, Xiao-Min Liu, Yuanhui Mao
 
 
 
Data Resources and Analyses
 
 
 
 
Comprehensive analysis of intramolecular G-quadruplex structures: furthering the understanding of their formalism border= 
 
Marc Farag, Liliane Mouawad
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
A super minigene with a short promoter and truncated introns recapitulates essential features of transcription and splicing regulation of the SMN1 and SMN2 genes border= 
 
Eric W Ottesen, Joonbae Seo, Diou Luo, Natalia N Singh, Ravindra N Singh
 
 
 
 
Genomic overview of INA-induced NPR1 targeting and transcriptional cascades in Arabidopsis border= 
 
Se-Hun Yun, Irfan Ullah Khan, Bosl Noh, Yoo-Sun Noh
 
 
 
Decoding the universal human chromatin landscape through teratoma-based profiling border= 
 
Benjamin L Kidder
 
 
 
Genomic transcription factor binding site selection is edited by the chromatin remodeling factor CHD4 border= 
 
Mika Saotome, Deepak B Poduval, Sara A Grimm, Aerica Nagornyuk, Sakuntha Gunarathna ...
 
 
 
Rat1 promotes premature transcription termination at R-loops border=  
 
José Antonio Mérida-Cerro, Pablo Maraver-Cárdenas, Ana G Rondón, Andrés Aguilera
 
 
 
Extending MeCP2 interactome: canonical nucleosomal histones interact with MeCP2 border= 
 
David Ortega-Alarcon, Rafael Claveria-Gimeno, Sonia Vega, Ladan Kalani, Olga C Jorge-Torres ...
 
 
 
 
Tet-mediated DNA methylation dynamics affect chromosome organization border= 
 
Hao Tian, Pengfei Luan, Yaping Liu, Guoqiang Li
 
 
 
LSD1 controls a nuclear checkpoint in Wnt/beta -Catenin signaling to regulate muscle stem cell self-renewal border= 
 
Sandrine Mouradian, Delia Cicciarello, Nicolas Lacoste, Valérie Risson, Francesca Berretta ...
 
 
 
Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development border= 
 
Marta Moreno-Oñate, Lourdes Gallardo-Fuentes, Pedro M Martínez-García, Silvia Naranjo, Sandra Jiménez-Gancedo ...
 
 
 
A circular RNA-gawky-chromatin regulatory axis modulates stress-induced transcription border= 
 
Rui Su, Min Zhou, Jiamei Lin, Ge Shan, Chuan Huang
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
Ccq1 restrains Mre11-mediated degradation to distinguish short telomeres from double-strand breaks border= 
 
Julien Audry, Haitao Zhang, Carly Kerr, Kathleen L Berkner, Kurt W Runge
 
 
 
The levels of p53 govern the hierarchy of DNA damage tolerance pathway usage border=  
 
Bryan A Castaño, Sabrina Schorer, Yitian Guo, Nicolás L Calzetta, Vanesa Gottifredi ...
 
 
 
NUDT16 regulates CtIP PARylation to dictate homologous recombination repair border=  
 
Zhen Zhang, William E Samsa, Zihua Gong
 
 
 
Human CST complex restricts excessive PrimPol repriming upon UV induced replication stress by suppressing p21 border= 
 
Pau Biak Sang, Rishi K Jaiswal, Xinxing Lyu, Weihang Chai
 
 
 
RPA interacts with Rad52 to promote meiotic crossover and noncrossover recombination border= 
 
Jeong H Joo, Soogil Hong, Mika T Higashide, Eui-Hwan Choi, Seobin Yoon ...
 
 
 
Unfilled gaps by polbeta lead to aberrant ligation by LIG1 at the downstream steps of base excision repair pathway border= 
 
Mitchell Gulkis, Ernesto Martinez, Danah Almohdar, Melike ÇaÄŸlayan
 
 
 
Genomics
 
 
 
 
The repertoire and structure of adhesion GPCR transcript variants assembled from publicly available deep-sequenced human samples border= 
 
Christina Katharina Kuhn, Udo Stenzel, Sandra Berndt, Ines Liebscher, Torsten Schöneberg ...
 
 
 
DNA fragility at topologically associated domain boundaries is promoted by alternative DNA secondary structure and topoisomerase II activity border= 
 
Heather M Raimer Young, Pei-Chi Hou, Anna R Bartosik, Naomi D Atkin, Lixin Wang ...
 
 
 
Uncovering the GacS-mediated role in evolutionary progression through trajectory reconstruction in Pseudomonas aeruginosa border= 
 
Bo Jiang, Huifang Qiu, Chenghui Lu, Mingqi Lu, Yuanhao Li ...
 
 
 
Molecular Biology
 
 
 
 
Blastocrithidia nonstop mitochondrial genome and its expression are remarkably insulated from nuclear codon reassignment border= 
 
Dmitry A Afonin, Evgeny S Gerasimov, Ingrid Å kodová-Sveráková, Kristína Záhonová, OndÅ™ej Gahura ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
Molecular basis of an atypical dsDNA 5mC/6mA bifunctional dioxygenase CcTet from Coprinopsis cinerea in catalyzing dsDNA 5mC demethylation border= 
 
Lin Zhang, Yajuan Mu, Tingting Li, Jingyan Hu, Houwen Lin ...
 
 
 
Retention of the RNA ends provides the molecular memory for maintaining the activation of the Csm complex border= 
 
Patrick Irmisch, Irmantas Mogila, Brighton Samatanga, Gintautas Tamulaitis, Ralf Seidel
 
 
 
Communication between DNA and nucleotide binding sites facilitates stepping by the RecBCD helicase border= 
 
Vera Gaydar, Rani Zananiri, Layla Saied, Or Dvir, Ariel Kaplan ...
 
 
 
Characterisation and engineering of a thermophilic RNA ligase from Palaeococcus pacificus border= 
 
Meghan Rousseau, Tifany Oulavallickal, Adele Williamson, Vic Arcus, Wayne M Patrick ...
 
 
 
An anticodon-sensing T-boxzyme generates the elongator nonproteinogenic aminoacyl-tRNA in situ of a custom-made translation system for incorporation border= 
 
Wei Lu, Naohiro Terasaka, Yuriko Sakaguchi, Takeo Suzuki, Tsutomu Suzuki ...
 
 
 
RNA and RNA-protein complexes
 
 
 
 
A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum border= 
 
Yan Zhu, Falk Ponath, Valentina Cosi, Jörg Vogel
 
 
 
RAVER1 hinders lethal EMT and modulates miR/RISC activity by the control of alternative splicing border= 
 
Alice Wedler, Nadine Bley, Markus Glaß, Simon Müller, Alexander Rausch ...
 
 
 
An evolutionarily conserved phosphoserine-arginine salt bridge in the interface between ribosomal proteins uS4 and uS5 regulates translational accuracy in Saccharomyces cerevisiae border= 
 
Kartikeya Joshi, Brooke Luisi, Grant Wunderlin, Sima Saleh, Anna Lilly ...
 
 
 
Tankyrase-1 regulates RBP-mediated mRNA turnover to promote muscle fiber formation border= 
 
Souad Mubaid, Brenda Janice Sanchez, Rinad A Algehani, Viktoriia Skopenkova, Pauline Adjibade ...
 
 
 
Evolving precision: rRNA expansion segment 7S modulates translation velocity and accuracy in eukaryal ribosomes border= 
 
Robert Rauscher, Cristian Eggers, Lyudmila Dimitrova-Paternoga, Vaishnavi Shankar, Alessia Rosina ...
 
 
 
Distinct functions for the paralogous RBM41 and U11/U12-65K proteins in the minor spliceosome border= 
 
Antto J Norppa, Iftekhar Chowdhury, Laura E van Rooijen, Janne J Ravantti, Berend Snel ...
 
 
 
Structural Biology
 
 
 
 
Mechanistic insights into the alternative ribosome recycling by HflXr border= 
 
Savannah M Seely, Ritwika S Basu, Matthieu G Gagnon
 
 
 
Structural basis of how MGME1 processes DNA 5² ends to maintain mitochondrial genome integrity border= 
 
Eric Y C Mao, Han-Yi Yen, Chyuan-Chuan Wu
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
Expanding the flexibility of base editing for high-throughput genetic screens in bacteria border= 
 
Sandra Gawlitt, Scott P Collins, Yanying Yu, Samuel A Blackman, Lars Barquist ...
 
 
 
Engineering an Escherichia coli strain for production of long single-stranded DNA border= 
 
Konlin Shen, Jake J Flood, Zhihuizi Zhang, Alvin Ha, Brian R Shy ...
 
 
 
Correction
 
 
 
 
Correction to ˜High fidelity DNA strand-separation is the major specificity determinant in DNA methyltransferase CcrM's catalytic mechanism' border= 
 
 
 
 
Correction to ˜Mechanistic insights into the alternative ribosome recycling by HflXr' border= 
 
 
 
 
Correction to ˜Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data' border= 
 
 
 
 
Methods
 
 
 
 
Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data border= 
 
Kevin Berg, Manivel Lodha, Isabel Delazer, Karolina Bartosik, Yilliam Cruz Garcia ...
 
 
 
Symmetry-breaking malachite green as a near-infrared light-activated fluorogenic photosensitizer for RNA proximity labeling border= 
 
Lan Li, Jinghua Han, Hei-Yong G Lo, Winnie Wai Ling Tam, Han Jia ...
 
 
 
Identification of G-quadruplex-interacting proteins in living cells using an artificial G4-targeting biotin ligase border= 
 
Ziang Lu, Shengjie Xie, Haomiao Su, Shaoqing Han, Haiyan Huang ...
 
 
 
Low-input and single-cell methods for Infinium DNA methylation BeadChips border=  
 
Sol Moe Lee, Christian E Loo, Rexxi D Prasasya, Marisa S Bartolomei, Rahul M Kohli ...
 
 
 
An autocatalytic CRISPR-Cas amplification effect propelled by the LNA-modified split activators for DNA sensing border= 
 
Ke Sun, Lei Pu, Chuan Chen, Mutian Chen, Kaiju Li ...
 
 
 
Exhaustive identification of genome-wide binding events of transcriptional regulators border= 
 
Anna Nordin, Pierfrancesco Pagella, Gianluca Zambanini, Claudio Cantù
 
 
Unsubscribe       Manage email alerts
 
Written requests to unsubscribe can be sent to: Journals Marketing, Oxford University Press, Great Clarendon Street, Oxford, OX2 6DP, UK.

Our Privacy Policy sets out how Oxford University Press handles your personal information.

The content of this email is protected by copyright.
 
Oxford University Press
 
 
                                 



This email is intended for bionet@evol.biology.mcmaster.ca.