Subject: Nucleic Acids Research Table of Contents for 22 July 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 13
 
22 July 2024
 
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Editorial
 
 
 
 
Editorial: Gary Felsenfeld (1929'2024) border= 
 
Thoru Pederson
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
YY1 is involved in homologous recombination inhibition at guanine quadruplex sites in human cells border= 
 
Xinyu Cui, Chengwen Zhang, Chunqing Fu, Jinglei Hu, Tengjiao Li ...
 
 
 
Formation of left-handed helices by C2²-fluorinated nucleic acids under physiological salt conditions border= 
 
Roberto El-Khoury, Cristina Cabrero, Santiago Movilla, Harneesh Kaur, David Friedland ...
 
 
 
Nanopores map the acid-base properties of a single site in a single DNA molecule border= 
 
Drew C Smith, Christopher A Thomas, Jonathan M Craig, Henry Brinkerhoff, Sarah J Abell ...
 
 
 
Promoter dependent RNA polymerase II bypass of the epimerizable DNA lesion, Fapy¢dG and 8-Oxo-2²-deoxyguanosine border= 
 
Shijun Gao, Yuki Tahara, Eric T Kool, Marc M Greenberg
 
 
 
 
 
Computational Biology
 
 
 
 
Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase border= 
 
Priti Roy, Zachary Walter, Lauren Berish, Holly Ramage, Martin McCullagh
 
 
 
Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA'ligand interactions border= 
 
Chandran Nithin, Sebastian Kmiecik, Roman BÅ‚aszczyk, Julita Nowicka, Irina TuszyÅ"ska
 
 
 
Data Resources and Analyses
 
 
 
 
A treasure trove of 1034 actinomycete genomes border= 
 
Tue Sparholt Jørgensen, Omkar S Mohite, Eva B Sterndorff, Maria Alvarez-Arevalo, Kai Blin ...
 
 
 
Refining the pool of RNA-binding domains advances the classification and prediction of RNA-binding proteins border= 
 
Elsa Wassmer, Gergely Koppány, Malte Hermes, Sven Diederichs, Maïwen Caudron-Herger
 
 
 
A comprehensive analysis of 3²UTRs in Caenorhabditis elegans border=  
 
Emma Murari, Dalton Meadows, Nicholas Cuda, Marco Mangone
 
 
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
Transposon DNA sequences facilitate the tissue-specific gene transfer of circulating tumor DNA between human cells border= 
 
Munevver Cinar, Lourdes Martinez-Medina, Pavan K Puvvula, Arsen Arakelyan, Badri N Vardarajan ...
 
 
 
Histone deacetylase Hos2 regulates protein expression noise by potentially modulating the protein translation machinery border= 
 
Wei-Han Lin, Florica J G Opoc, Chia-Wei Liao, Kevin R Roy, Lars M Steinmetz ...
 
 
 
Repression of pervasive antisense transcription is the primary role of fission yeast RNA polymerase II CTD serine 2 phosphorylation border= 
 
Cédric Boulanger, Nouhou Haidara, Carlo Yague-Sanz, Marc Larochelle, Pierre-Étienne Jacques ...
 
 
 
IRF2BP2 counteracts the ATF7/JDP2 AP-1 heterodimer to prevent inflammatory overactivation in acute myeloid leukemia (AML) cells border= 
 
Sabrina Fischer, Lisa Marie Weber, Bastian Stielow, Miriam Frech, Clara Simon ...
 
 
 
The developmental and evolutionary characteristics of transcription factor binding site clustered regions based on an explainable machine learning model border= 
 
Zhangyi Ouyang, Feng Liu, Wanying Li, Junting Wang, Bijia Chen ...
 
 
 
Genomic context-dependent histone H3K36 methylation by three Drosophila methyltransferases and implications for dedicated chromatin readers border= 
 
Muhunden Jayakrishnan, Magdalena Havlová, Václav Veverka, Catherine Regnard, Peter B Becker
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
Replication protein A dynamically re-organizes on primer/template junctions to permit DNA polymerase delta holoenzyme assembly and initiation of DNA synthesis border= 
 
Jessica L Norris, Lindsey O Rogers, Kara G Pytko, Rachel L Dannenberg, Samuel Perreault ...
 
 
 
KDM6A'SND1 interaction maintains genomic stability by protecting the nascent DNA and contributes to cancer chemoresistance border= 
 
Jian Wu, Yixin Jiang, Qin Zhang, Xiaobing Mao, Tong Wu ...
 
 
 
RAD18 directs DNA double-strand break repair by homologous recombination to post-replicative chromatin border= 
 
Matous Palek, Natalie Palkova, Marta Cerna, Klara Horackova, Milena Hovhannisyan ...
 
 
 
Binding of the TRF2 iDDR motif to RAD50 highlights a convergent evolutionary strategy to inactivate MRN at telomeres border= 
 
Freddy Khayat, Majedh Alshmery, Mohinder Pal, Antony W Oliver, Alessandro Bianchi
 
 
 
Genomics
 
 
 
 
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing border= 
 
Ritu Shekhar, Tina O'Grady, Netanya Keil, April Feswick, David A Moraga Amador ...
 
 
 
ONECUT2 acts as a lineage plasticity driver in adenocarcinoma as well as neuroendocrine variants of prostate cancer border= 
 
Chen Qian, Qian Yang, Mirja Rotinen, Rongrong Huang, Hyoyoung Kim ...
 
 
 
Molecular Biology
 
 
 
 
Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes border= 
 
John B Moldovan, Huira C Kopera, Ying Liu, Marta Garcia-Canadas, Purificacion Catalina ...
 
 
 
Phage-host co-evolution has led to distinct generalized transduction strategies border= 
 
Sanne Wolput, Cédric Lood, Alfred Fillol-Salom, Yorben Casters, Alaa Albasiony ...
 
 
 
The impact of mRNA poly(A) tail length on eukaryotic translation stages border=  
 
Nikita Biziaev, Alexey Shuvalov, Ali Salman, Tatiana Egorova, Ekaterina Shuvalova ...
 
 
 
Intrinsically disordered regions regulate RhlE RNA helicase functions in bacteria border= 
 
Stéphane Hausmann, Johan Geiser, George Edward Allen, Sandra Amandine Marie Geslain, Martina Valentini
 
 
 
Nucleic Acid Enzymes
 
 
 
 
Eukaryotic AlaX provides multiple checkpoints for quality and quantity of aminoacyl-tRNAs in translation border= 
 
Zi-Han Li, Xiao-Long Zhou
 
 
 
A Plasmodium apicoplast-targeted unique exonuclease/FEN exhibits interspecies functional differences attributable to an insertion that alters DNA-binding border= 
 
Tribeni Chatterjee, Anupama Tiwari, Ritika Gupta, Himadri Shukla, Aastha Varshney ...
 
 
 
Coordinated DNA polymerization by Polgamma and the region of LonP1 regulated proteolysis 
 
Amanda A Riccio, Asia J Brannon, Juno M Krahn, Jonathan Bouvette, Jason G Williams ...
 
 
 
RNA and RNA-protein complexes
 
 
 
 
A novel regulatory interplay between atypical B12 riboswitches and uORF translation in Mycobacterium tuberculosis border= 
 
Terry Kipkorir, Peter Polgar, Declan Barker, Alexandre D'Halluin, Zaynah Patel ...
 
 
 
The uS10c-BPG2 module mediates ribosomal RNA processing in chloroplast nucleoids border= 
 
Xueping Sun, Meenu Singla-Rastogi, Jingwen Wang, Chuanzhi Zhao, Xingjun Wang ...
 
 
 
Genome-wide analysis of mRNA decay in Arabidopsis shoot and root reveals the importance of co-translational mRNA decay in the general mRNA turnover border= 
 
Marie-Christine Carpentier, Anne-Elodie Receveur, Alexandre Boubegtitene, Adrien Cadoudal, Cécile Bousquet-Antonelli ...
 
 
 
Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress border= 
 
Attila Horvath, Yoshika Janapala, Katrina Woodward, Shafi Mahmud, Alice Cleynen ...
 
 
 
Structural Biology
 
 
 
 
YjgA plays dual roles in enhancing PTC maturation border= 
 
Mengtan Du, Chenke Deng, Ting Yu, Qixin Zhou, Fuxing Zeng
 
 
 
Crystal structure of a tetrameric RNA G-quadruplex formed by hexanucleotide repeat expansions of C9orf72 in ALS/FTD border= 
 
Yanyan Geng, Changdong Liu, Naining Xu, Monica Ching Suen, Haitao Miao ...
 
 
 
The 5²-terminal stem'loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH border= 
 
Sabrina Toews, Anna Wacker, Edgar M Faison, Elke Duchardt-Ferner, Christian Richter ...
 
 
 
Cooperative Gsx2'DNA binding requires DNA bending and a novel Gsx2 homeodomain interface border= 
 
Jordan A Webb, Edward Farrow, Brittany Cain, Zhenyu Yuan, Alexander E Yarawsky ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
OptoLacI: optogenetically engineered lactose operon repressor LacI responsive to light instead of IPTG border= 
 
Meizi Liu, Zuhui Li, Jianfeng Huang, Junjun Yan, Guoping Zhao ...
 
 
 
Engineering spacer specificity of the Cre/loxP system border=  
 
Jenna Hoersten, Gloria Ruiz-Gómez, Maciej Paszkowski-Rogacz, Giorgio Gilioli, Pedro Manuel Guillem-Gloria ...
 
 
 
Corrections
 
 
 
 
Correction to ˜YASS: enhancing the sensitivity of DNA similarity search' border= 
 
 
 
 
Correction to ˜N2-methylguanosine modifications on human tRNAs and snRNA U6 are important for cell proliferation, protein translation and pre-mRNA splicing' border= 
 
 
 
 
Correction to ˜hnRNPA1 couples nuclear export and translation of specific mRNAs downstream of FGF-2/S6K2 signalling' border= 
 
 
 
 
Correction to ˜Overexpression of eIF5 or its protein mimic 5MP perturbs eIF2 function and induces ATF4 translation through delayed re-initiation' border= 
 
 
 
 
Correction to ˜Structure of an internal loop motif with three consecutive U·U mismatches from stem'loop 1 in the 3²-UTR of the SARS-CoV-2 genomic RNA' border=  
 
 
 
 
Correction to ˜Cooperative Gsx2'DNA binding requires DNA bending and a novel Gsx2 homeodomain interface' border= 
 
 
 
 
Correction to ˜KDM6A'SND1 interaction maintains genomic stability by protecting the nascent DNA and contributes to cancer chemoresistance' border= 
 
 
 
 
Methods
 
 
 
 
Induro-RT mediated circRNA-sequencing (IMCR-seq) enables comprehensive profiling of full-length and long circular RNAs from low input total RNA border= 
 
Irem Unlu, Sean Maguire, Shengxi Guan, Zhiyi Sun
 
 
 
iSuRe-HadCre is an essential tool for effective conditional genetics border=  
 
Irene Garcia-Gonzalez, Susana F Rocha, Anahita Hamidi, Lourdes Garcia-Ortega, Alvaro Regano ...
 
 
 
CAbiNet: joint clustering and visualization of cells and genes for single-cell transcriptomics border= 
 
Yan Zhao, Clemens Kohl, Daniel Rosebrock, Qinan Hu, Yuhui Hu ...
 
 
 
Transfer learning for cross-context prediction of protein expression from 5'UTR sequence border= 
 
Pierre-Aurélien Gilliot, Thomas E Gorochowski
 
 
 
FRET-guided modeling of nucleic acids border=  
 
Fabio D Steffen, Richard A Cunha, Roland K O Sigel, Richard Börner
 
 
 
Reinventing gene expression connectivity through regulatory and spatial structural empowerment via principal node aggregation graph neural network border= 
 
Fengyao Yan, Limin Jiang, Danqian Chen, Michele Ceccarelli, Yan Guo
 
 
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