Subject: Nucleic Acids Research Table of Contents for 28 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 4
 
28 February 2024
 
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NAR Breakthrough Article
 
 
 
 
Gene-to-gene coordinated regulation of transcription and alternative splicing by 3D chromatin remodeling upon NF-kappa B activation border= 
 
Paul Marie, Matéo Bazire, Julien Ladet, Lamya Ben Ameur, Sanjay Chahar ...
 
 
 
Critical Reviews and Perspectives
 
 
 
 
The miRNA'target interactions: An underestimated intricacy border= 
 
Caroline Diener, Andreas Keller, Eckart Meese
 
 
 
To kill a microRNA: emerging concepts in target-directed microRNA degradation border=  
 
Amber F Buhagiar, Benjamin Kleaveland
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
Extracellular G-quadruplexes and Z-DNA protect biofilms from DNase I, and G-quadruplexes form a DNAzyme with peroxidase activity border= 
 
Gabriel Antonio Salvador Minero, Andreas Møllebjerg, Celine Thiesen, Mikkel Illemann Johansen, Nis Pedersen Jørgensen ...
 
 
 
Dimeric structures of DNA ATTTC repeats promoted by divalent cations border=  
 
Marko Trajkovski, Annalisa Pastore, Janez Plavec
 
 
 
 
 
Computational Biology
 
 
 
 
Reconstructing DNA methylation maps of ancient populations border= 
 
Arielle Barouch, Yoav Mathov, Eran Meshorer, Benjamin Yakir, Liran Carmel
 
 
 
Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework border= 
 
Jiayi Liu, Tal Ashuach, Fumitaka Inoue, Nadav Ahituv, Nir Yosef ...
 
 
 
Data Resources and Analyses
 
 
 
 
CMC: Cancer miRNA Census ' a list of cancer-related miRNA genes border= 
 
Malwina Suszynska, Magdalena Machowska, Eliza Fraszczyk, Maciej Michalczyk, Anna Philips ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
Lysine acetylation regulates the AT-rich DNA possession ability of H-NS border= 
 
Yabo Liu, Mengqing Zhou, Yifan Bu, Liang Qin, Yuanxing Zhang ...
 
 
 
A bromodomain-independent mechanism of gene regulation by the BET inhibitor JQ1: direct activation of nuclear receptor PXR border= 
 
Andrew D Huber, Shyaron Poudel, Jing Wu, Darcie J Miller, Wenwei Lin ...
 
 
 
 
Single-molecule visualization of twin-supercoiled domains generated during transcription border= 
 
Richard Janissen, Roman Barth, Minco Polinder, Jaco van der Torre, Cees Dekker
 
 
 
The cysteine-rich domain in CENP-A chaperone Scm3HJURP ensures centromere targeting and kinetochore integrity 
 
H Diego Folco, Hua Xiao, David Wheeler, Hanqiao Feng, Yawen Bai ...
 
 
 
Enhancer'promoter interactions can form independently of genomic distance and be functional across TAD boundaries border= 
 
Deevitha Balasubramanian, Pedro Borges Pinto, Alexia Grasso, Séverine Vincent, Hélène Tarayre ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
Analysis of cytosine deamination events in excision repair sequencing reads reveals mechanisms of incision site selection in NER border= 
 
Benjamin Morledge-Hampton, Ananth Kalyanaraman, John J Wyrick
 
 
 
Quantitative, titratable and high-throughput reporter assays to measure DNA double strand break repair activity in cells border= 
 
Eeson Rajendra, Diego Grande, Bethany Mason, Daniela Di Marcantonio, Lucy Armstrong ...
 
 
 
Rrm3 and Pif1 division of labor during replication through leading and lagging strand G-quadruplex border= 
 
Mor Varon, Daniel Dovrat, Jonathan Heuzé, Ioannis Tsirkas, Saurabh P Singh ...
 
 
 
BG4 antibody can recognize telomeric G-quadruplexes harboring destabilizing base modifications and lesions border= 
 
Samuel A Johnson, Tapas Paul, Samantha L Sanford, Brittani L Schnable, Ariana C Detwiler ...
 
 
 
Genomics
 
 
 
 
Mutational profile of the regenerative process and de novo genome assembly of the planarian Schmidtea polychroa border= 
 
Ádám Póti, Dávid Szüts, Jelena Vermezovic
 
 
 
Genomic profiling of six human somatic histone H1 variants denotes that H1X accumulates at recently incorporated transposable elements border= 
 
Mónica Salinas-Pena, Núria Serna-Pujol, Albert Jordan
 
 
 
Molecular Biology
 
 
 
 
Kaposi's sarcoma herpesvirus exploits the DNA damage response to circularize its genome border= 
 
Shijun Li, Bing Liu, Min Tan, Franceline Juillard, Agnieszka Szymula ...
 
 
 
Multiple mechanisms activate GCN2 eIF2 kinase in response to diverse stress conditions border= 
 
Jagannath Misra, Kenneth R Carlson, Dan F Spandau, Ronald C Wek
 
 
 
Single-cell evidence for plasmid addiction mediated by toxin'antitoxin systems border= 
 
Nathan Fraikin, Laurence Van Melderen
 
 
 
Nucleic Acid Enzymes
 
 
 
 
Two-motif model illuminates DICER cleavage preferences border= 
 
Cong Truc Le, Trung Duc Nguyen, Tuan Anh Nguyen
 
 
 
Molecular mechanism of human ISG20L2 for the ITS1 cleavage in the processing of 18S precursor ribosomal RNA border= 
 
Yinliang Ma, Jiaxu Wang, Xingyi He, Yuhang Liu, Shuo Zhen ...
 
 
 
Conversion of the CG specific M.MpeI DNA methyltransferase into an enzyme predominantly methylating CCA and CCC sites border= 
 
Pál Albert, Bence Varga, Györgyi Ferenc, Antal Kiss
 
 
 
Toxin release by conditional remodelling of ParDE1 from Mycobacterium tuberculosis leads to gyrase inhibition border= 
 
Izaak N Beck, Tom J Arrowsmith, Matthew J Grobbelaar, Elizabeth H C Bromley, Jon Marles-Wright ...
 
 
 
RNA and RNA-protein complexes
 
 
 
 
Nuclear localization of Argonaute 2 is affected by cell density and may relieve repression by microRNAs border= 
 
Krystal C Johnson, Audrius Kilikevicius, Cristina Hofman, Jiaxin Hu, Yang Liu ...
 
 
 
GPATCH4 regulates rRNA and snRNA 2²-O -methylation in both DHX15-dependent and DHX15-independent manners border= 
 
Nidhi Kanwal, Nicolai Krogh, Indira Memet, Nicolas Lemus-Diaz, Chairini C Thomé ...
 
 
 
The RNA helicase Dbp10 coordinates assembly factor association with PTC maturation during ribosome biogenesis border= 
 
Valentin Mitterer, Hussein Hamze, Natalia Kunowska, Ulrich Stelzl, Anthony K Henras ...
 
 
 
Discovery of novel microRNA mimic repressors of ribosome biogenesis border=  
 
Carson J Bryant, Mason A McCool, Gabriela T Rosado González, Laura Abriola, Yulia V Surovtseva ...
 
 
 
Structural Biology
 
 
 
 
Target DNA-dependent activation mechanism of the prokaryotic immune system SPARTA border= 
 
Giada Finocchio, Balwina Koopal, Ana Potocnik, Clint Heijstek, Adrie H Westphal ...
 
 
 
Checkpoint activation by Spd1: a competition-based system relying on tandem disordered PCNA binding motifs border= 
 
Johan G Olsen, Andreas Prestel, Noah Kassem, Sebastian S Broendum, Hossain Mohammad Shamim ...
 
 
 
Flexible structural arrangement and DNA-binding properties of protein p6 from Bacillus subtillis phage φ29 border= 
 
Martín Alcorlo, Juan Román Luque-Ortega, Federico Gago, Alvaro Ortega, Milagros Castellanos ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
Intein-based thermoregulated meganucleases for containment of genetic material border= 
 
Gary W Foo, Christopher D Leichthammer, Ibrahim M Saita, Nicholas D Lukas, Izabela Z Batko ...
 
 
 
Cooperativity between Cas9 and hyperactive AID establishes broad and diversifying mutational footprints in base editors border= 
 
Kiara N Berríos, Aleksia Barka, Jasleen Gill, Juan C Serrano, Peter F Bailer ...
 
 
 
Correction
 
 
 
 
Correction to ˜Mapping the LINE1 ORF1 protein interactome reveals associated inhibitors of human retrotransposition' border= 
 
 
 
 
Correction to ˜Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome' border= 
 
 
 
 
Methods
 
 
 
 
HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data border=  
 
Haowei Du, Zain Dardas, Angad Jolly, Christopher M Grochowski, Shalini N Jhangiani ...
 
 
 
The pAblo· pCasso self-curing vector toolset for unconstrained cytidine and adenine base-editing in Gram-negative bacteria border= 
 
Ekaterina Kozaeva, Zacharias S Nielsen, Manuel Nieto-Domínguez, Pablo I Nikel
 
 
 
Less-is-more: selecting transcription factor binding regions informative for motif inference border= 
 
Jinrui Xu, Jiahao Gao, Pengyu Ni, Mark Gerstein
 
 
 
Improved detection and consistency of RNA-interacting proteomes using DIA SILAC border= 
 
Thomas C J Tan, Christos Spanos, David Tollervey
 
 
 
Visualizing DNA single- and double-strand breaks in the Flash comet assay by DNA polymerase-assisted end-labelling border= 
 
Erik Bivehed, Björn Hellman, Leonie Wenson, Bo Stenerlöw, Ola Söderberg ...
 
 
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