Subject: Nucleic Acids Research Table of Contents for 9 September 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 16
 
9 September 2024
 
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NAR Breakthrough Article
 
 
 
 
CRISPR-Cas12a exhibits metal-dependent specificity switching border= 
 
Giang T Nguyen, Michael A Schelling, Akshara Raju, Kathryn A Buscher, Aneisha Sritharan ...
 
 
 
Critical Reviews and Perspectives
 
 
 
 
A new perspective on microRNA-guided gene regulation specificity, and its potential generalization to transcription factors and RNA-binding proteins border= 
 
Hervé Seitz
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
High ionic strength vector formulations enhance gene transfer to airway epithelia border= 
 
Ashley L Cooney, Laura Marquez Loza, Kenan Najdawi, Christian M Brommel, Paul B McCray, Jr. ...
 
 
 
RNA encoded peptide barcodes enable efficient in vivo screening of RNA delivery systems border= 
 
Uchechukwu Odunze, Nitin Rustogi, Paul Devine, Lorraine Miller, Sara Pereira ...
 
 
 
Solution structures and effects of a platinum compound successively bound MYC G-quadruplex border= 
 
Wenting Liu, Bo-Chen Zhu, Liu-Yi Liu, Xiao- Yu Xia, Jinho Jang ...
 
 
 
 
Understanding the relationship between sequences and kinetics of DNA strand displacements border= 
 
Da Long, Peichen Shi, Xin Xu, Jiayi Ren, Yuqing Chen ...
 
 
 
Computational Biology
 
 
 
 
CoPixie, a novel algorithm for single-particle track colocalization, enables efficient quantification of telomerase dynamics at telomeres border= 
 
Samuel Prince, Kamélia Maguemoun, Mouna Ferdebouh, Emmanuelle Querido, Amélie Derumier ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
Small RNA-mediated genetic switches coordinate ALG-3/4 small RNA pathway function border= 
 
Trilotma Sen, Cara McCormick, Alicia K Rogers
 
 
 
SMCHD1 activates the expression of genes required for the expansion of human myoblasts border= 
 
Matthew Man-Kin Wong, Sarah Hachmer, Ed Gardner, Valeria Runfola, Eric Arezza ...
 
 
 
BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1A border= 
 
Takayuki Hoshii, Sota Kikuchi, Tomoya Kujirai, Takeshi Masuda, Tomoko Ito ...
 
 
 
 
Adenovirus small E1A directs activation of Alu transcription at YAP/TEAD- and AP-1-bound enhancers through interactions with the EP400 chromatin remodeler border= 
 
Simona Cantarella, Marco Vezzoli, Davide Carnevali, Marco Morselli, Nathan R Zemke ...
 
 
 
ADBP-1 regulates ADR-2 nuclear localization to control editing substrate selection border= 
 
Berta Eliad, Noa Schneider, Orna Ben-Naim Zgayer, Yarden Amichan, Fabian Glaser ...
 
 
 
Central role of SUMOylation in the regulation of chromatin interactions and transcriptional outputs of the androgen receptor in prostate cancer cells border= 
 
Kaisa-Mari Launonen, Vera Varis, Niina Aaltonen, Einari A Niskanen, Markku Varjosalo ...
 
 
 
H3T11 phosphorylation by CKII is required for heterochromatin formation in Neurospora border= 
 
Yuan Tian, Chengcheng Zhang, Xiang Tian, Lu Zhang, Tong Yin ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
DNA cytosine methyltransferases differentially regulate genome-wide hypermutation and interhomolog recombination in Trichoderma reesei meiosis border= 
 
Lavernchy Jovanska, I-Chen Lin, Jhong-Syuan Yao, Chia-Ling Chen, Hou-Cheng Liu ...
 
 
 
Instability throughout the Saccharomyces cerevisiae genome resulting from Pms1 endonuclease deficiency 
 
Scott A Lujan, Marta A Garbacz, Sascha E Liberti, Adam B Burkholder, Thomas A Kunkel
 
 
 
The critical role of the iron'sulfur cluster and CTC components in DOG-1/BRIP1 function in Caenorhabditis elegans border= 
 
Xiao Li, Ivette Maria Menendez Perdomo, Victoria Rodrigues Alves Barbosa, Catherine Diao, Maja Tarailo-Graovac
 
 
 
Differential processing of RNA polymerase II at DNA damage correlates with transcription-coupled repair syndrome severity border= 
 
Camila Gonzalo-Hansen, Barbara Steurer, Roel C Janssens, Di Zhou, Marjolein van Sluis ...
 
 
 
The translesion polymerase Pol Y1 is a constitutive component of the B. subtilis replication machinery border= 
 
McKayla E Marrin, Michael R Foster, Chloe M Santana, Yoonhee Choi, Avtar S Jassal ...
 
 
 
Loss of the DNA repair protein, polynucleotide kinase/phosphatase, activates the type 1 interferon response independent of ionizing radiation border= 
 
Wisdom Deebeke Kate, Mesfin Fanta, Michael Weinfeld
 
 
 
The cullin Rtt101 promotes ubiquitin-dependent DNAâˆ'protein crosslink repair across the cell cycle border= 
 
Audrey Noireterre, Julien Soudet, Ivona Bagdiul, Françoise Stutz
 
 
 
Molecular Biology
 
 
 
 
A UTP3-dependent nucleolar translocation pathway facilitates pre-rRNA 5²ETS processing border= 
 
Jiayang Bao, Baochun Su, Zheyan Chen, Zhaoxiang Sun, Jinrong Peng ...
 
 
 
TRF2'RAP1 represses RAD51-dependent homology-directed telomere repair by promoting BLM-mediated D-loop unwinding and inhibiting BLM'DNA2-dependent 5²-end resection border= 
 
Fengshan Liang, Rekha Rai, Tori Sodeinde, Sandy Chang
 
 
 
The human mitochondrial translation factor TACO1 alleviates mitoribosome stalling at polyproline stretches border= 
 
Michele Brischigliaro, Annika Krüger, J Conor Moran, Hana Antonicka, Ahram Ahn ...
 
 
 
Molecular basis of RNA recombination in the 3²UTR of chikungunya virus genome border=  
 
Eugenia S Bardossy, Sebastiano Volpe, Yasutsugu Suzuki, Fernando Merwaiss, Santiago Faraj ...
 
 
 
Stress granule formation helps to mitigate neurodegeneration border=  
 
M Rebecca Glineburg, Evrim Yildirim, Nicolas Gomez, Genesis Rodriguez, Jaclyn Pak ...
 
 
 
Discovery of antiphage systems in the lactococcal plasmidome border=  
 
Andriana Grafakou, Cas Mosterd, Matthias H Beck, Philip Kelleher, Brian McDonnell ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
Highly sensitive mapping of in vitro type II topoisomerase DNA cleavage sites with SHAN-seq 
 
Ian L Morgan, Shannon J McKie, Rachel Kim, Yeonee Seol, Jing Xu ...
 
 
 
Structural insights into the assembly of type IIA topoisomerase DNA cleavage-religation center border= 
 
Ko-Ting Liu, Shin-Fu Chen, Nei-Li Chan
 
 
 
The complete pathway for co-transcriptional mRNA maturation within a large protein of a non-segmented negative-strand RNA virus border= 
 
Minako Ogino, Todd J Green, Tomoaki Ogino
 
 
 
RNA and RNA-protein complexes
 
 
 
 
Mapping the structural landscape of the yeast Ty3 retrotransposon RNA genome border= 
 
Angelika Andrzejewska-Romanowska, Julita Gumna, Ewa TykwiÅ"ska, Katarzyna Pachulska-Wieczorek
 
 
 
Structure and RNA-binding of the helically extended Roquin CCCH-type zinc finger border= 
 
Jan-Niklas Tants, Lasse Oberstrass, Julia E Weigand, Andreas Schlundt
 
 
 
Resolution of ribosomal stalling by EF-P and ABCF ATPases YfmR and YkpA/YbiT border=  
 
Hiraku Takada, Keigo Fujiwara, Gemma C Atkinson, Shinobu Chiba, Vasili Hauryliuk
 
 
 
RESC14 and RESC8 cooperate to mediate RESC function and dynamics during trypanosome RNA editing border= 
 
Katherine Wackowski, Xiaoyu Zhu, Shichen Shen, Ming Zhang, Jun Qu ...
 
 
 
Phosphorylation of the nuclear poly(A) binding protein (PABPN1) during mitosis protects mRNA from hyperadenylation and maintains transcriptome dynamics border= 
 
Jackson M Gordon, David V Phizicky, Leonard Schärfen, Courtney L Brown, Dahyana Arias Escayola ...
 
 
 
Asymmetric bulges within hairpin RNA transgenes influence small RNA size, secondary siRNA production and viral defence border= 
 
Daai Zhang, Dengwei Jue, Neil Smith, Chengcheng Zhong, E Jean Finnegan ...
 
 
 
Loss of Lamin A leads to the nuclear translocation of AGO2 and compromised RNA interference border= 
 
Vivian Lobo, Iwona Nowak, Carola Fernandez, Ana Iris Correa Muler, Jakub O Westholm ...
 
 
 
CyCoNP lncRNA establishes cis and trans RNA'RNA interactions to supervise neuron physiology border= 
 
Fabio Desideri, Alessandro Grazzi, Michela Lisi, Adriano Setti, Tiziana Santini ...
 
 
 
Structural Biology
 
 
 
 
High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping border= 
 
Bret Lange, Ricardo G Gil, Gavin S Anderson, Joseph D Yesselman
 
 
 
Unraveling the structure and function of a novel SegC protein interacting with the SegAB chromosome segregation complex in Archaea border= 
 
Min-Guan Lin, Cheng-Yi Yen, Yo-You Shen, Yu-Sung Huang, Irene W Ng ...
 
 
 
Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch border=  
 
Chad W Hicks, Sanim Rahman, Susan L Gloor, James K Fields, Natalia Ledo Husby ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
Engineered transcription activator-like effector dimer proteins confer DNA loop-dependent gene repression comparable to Lac repressor border= 
 
Nicole A Becker, Justin P Peters, Elizabeth Lewis, Camden L Daby, Karl Clark ...
 
 
 
CRISPR perfect adaptation for robust control of cellular immune and apoptotic responses border= 
 
Yichi Zhang, Shuyi Zhang
 
 
 
Induction of bacterial expression at the mRNA level by light border=  
 
Américo T Ranzani, Konrad Buchholz, Marius Blackholm, Hayat Kopkin, Andreas Möglich
 
 
 
Methods
 
 
 
 
Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data border= 
 
Bernhard C Thiel, Giovanni Bussi, Simón Poblete, Ivo L Hofacker
 
 
 
GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs border= 
 
Jianshu Zhao, Jean Pierre Both, Luis M Rodriguez-R, Konstantinos T Konstantinidis
 
 
 
CLOCI: unveiling cryptic fungal gene clusters with generalized detection border=  
 
Zachary Konkel, Laura Kubatko, Jason C Slot
 
 
 
MADDD-seq, a novel massively parallel sequencing tool for simultaneous detection of DNA damage and mutations border= 
 
Marc Vermulst, Samantha L Paskvan, Claire S Chung, Kathryn Franke, Nigel Clegg ...
 
 
 
HYENA detects oncogenes activated by distal enhancers in cancer border=  
 
Anqi Yu, Ali E Yesilkanal, Ashish Thakur, Fan Wang, Yang Yang ...
 
 
 
Quantifying allele-specific CRISPR editing activity with CRISPECTOR2.0 border=  
 
Guy Assa, Nechama Kalter, Michael Rosenberg, Avigail Beck, Oshry Markovich ...
 
 
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