Subject: Nucleic Acids Research Table of Contents for 14 October 2024 Oxford Academic
 
 
 
Oxford Academic
 
 
 
 
New issue alert
 
 
 
 
NAR Invites Submissions for the 2025 Web Server Issue
 

In July of each year, NAR devotes a single issue to papers describing web-based software resources of value to the biological community. This issue focuses on web servers offering computations for DNA, RNA, and protein sequences, high-throughput sequencing data, and biological network analysis, and includes a special section for Web Services. The deadline for submitting your proposal is 20th December. 

Explore the full guidelines and submit your work
 
 
 
 
Nucleic Acids Research  
Volume 52 Issue 18
 
14 October 2024
 
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NAR Breakthrough Article
 
 
 
 
Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein'protein interactions border= 
 
Ziyuan Chen, Melissa Seman, Yekaterina Fyodorova, Ali Farhat, Amanda Ames ...
 
 
 
Critical Reviews and Perspectives
 
 
 
 
Striving for clarity in language about gene expression  
 
Ana S G Cunningham, Myriam Gorospe
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
Synthesis of 2²-formamidonucleoside phosphoramidites for suppressing the seed-based off-target effects of siRNAs border= 
 
Kohei Nomura, Seongjin An, Yoshiaki Kobayashi, Jiro Kondo, Ting Shi ...
 
 
 
Modulation of dynamic DNA G-quadruplex structures in the hTERT promoter region by ligands border= 
 
Deepak Karna, Lin Liang, Grinsun Sharma, Shankar Mandal, Sefan Asamitsu ...
 
 
 
Trinucleotide cap analogs with triphosphate chain modifications: synthesis, properties, and evaluation as mRNA capping reagents border= 
 
Marcin Warminski, Anais Depaix, Kamil Ziemkiewicz, Tomasz Spiewla, Joanna Zuberek ...
 
 
 
 
Identification of an RNA-binding perturbing characteristic for thiopurine drugs and their derivatives to disrupt CELF1'RNA interaction border= 
 
Yang Tan, Zhibo Zhao, Qingfang Han, Peipei Xu, Xiaopeng Shen ...
 
 
 
Computational Biology
 
 
 
 
Unlocking precision in aptamer engineering: a case study of the thrombin binding aptamer illustrates why modification size, quantity, and position matter border= 
 
Makay T Murray, Stacey D Wetmore
 
 
 
Machine learning unravels inherent structural patterns in Escherichia coli Hi-C matrices and predicts chromosome dynamics border= 
 
Palash Bera, Jagannath Mondal
 
 
 
ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment border= 
 
Davyd R Bohdan, Janusz M Bujnicki, Eugene F Baulin
 
 
 
SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions border= 
 
Axel Fehrenbach, Alexander Mitrofanov, Omer S Alkhnbashi, Rolf Backofen, Franz Baumdicker
 
 
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
ALKBH5 governs human endoderm fate by regulating the DKK1/4-mediated Wnt/beta -catenin activation border= 
 
Zechuan Liang, Tao Huang, Wei Li, Zhaoyi Ma, Kaipeng Wang ...
 
 
 
Unexpected nuclear hormone receptor and chromatin dynamics regulate estrous cycle dependent gene expression 
 
Wendy N Jefferson, Tianyuan Wang, Elizabeth Padilla-Banks, Carmen J Williams
 
 
 
Heterochromatin protein 1 alpha (HP1alpha ) undergoes a monomer to dimer transition that opens and compacts live cell genome architecture border= 
 
Jieqiong Lou, Qiji Deng, Xiaomeng Zhang, Charles C Bell, Andrew B Das ...
 
 
 
The impact of the embryonic DNA methylation program on CTCF-mediated genome regulation border= 
 
Ana Monteagudo-Sánchez, Julien Richard Albert, Margherita Scarpa, Daan Noordermeer, Maxim V C Greenberg
 
 
 
DipR, a GntR/FadR-family transcriptional repressor: regulatory mechanism and widespread distribution of the dip cluster for dipicolinic acid catabolism in bacteria border= 
 
Yinhu Jiang, Kexin Wang, Lu Xu, Lanyi Xu, Qimiao Xu ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
Loss of DNA glycosylases improves health and cognitive function in a C. elegans model of human tauopathy 
 
Vinod Tiwari, Elisabeth Buvarp, Fivos Borbolis, Chandrakala Puligilla, Deborah L Croteau ...
 
 
 
Dispensability of HPF1 for cellular removal of DNA single-strand breaks border=  
 
Kristyna Hrychova, Kamila Burdova, Zuzana Polackova, Despoina Giamaki, Beatrice Valtorta ...
 
 
 
Replication fork stalling in late S-phase elicits nascent strand degradation by DNA mismatch repair border= 
 
Erica Colicino-Murbach, Caitlin Hathaway, Huzefa Dungrawala
 
 
 
Second generation lethality in RNAseH2a knockout zebrafish border=  
 
Ruth C Thomas, Ringaile Zaksauskaite, Norah Y Al-Kandari, Anne Cathrine Hyde, Arwa A Abugable ...
 
 
 
Mechanism of structure-specific DNA binding by the FANCM branchpoint translocase border= 
 
Lara Abbouche, Vincent J Murphy, Jixuan Gao, Sylvie van Twest, Alexander P Sobinoff ...
 
 
 
Genomics
 
 
 
 
Long range segmentation of prokaryotic genomes by gene age and functionality  
 
Yuri I Wolf, Ilya V Schurov, Kira S Makarova, Mikhail I Katsnelson, Eugene V Koonin
 
 
 
Molecular and Structural Biology
 
 
 
 
HIV-1 usurps mixed-charge domain-dependent CPSF6 phase separation for higher-order capsid binding, nuclear entry and viral DNA integration border= 
 
Sooin Jang, Gregory J Bedwell, Satya P Singh, Hyun Jae Yu, Bjarki Arnarson ...
 
 
 
Structural insights into the biosynthetic mechanism of Nalpha -GlyT and 5-N mdU hypermodifications of DNA border= 
 
Yan Wen, Wenting Guo, Chunyan Meng, Jie Yang, Sha Xu ...
 
 
 
How to scan naked DNA using promiscuous recognition and no clamping: a model for pioneer transcription factors border= 
 
Rama Reddy Goluguri, Catherine Ghosh, Joshua Quintong, Mourad Sadqi, Victor Muñoz
 
 
 
Crystal structure and nucleic acid binding mode of CPV NSP9: implications for viroplasm in Reovirales border= 
 
Yeda Wang, Hangtian Guo, Yuhao Lu, Wanbin Yang, Tinghan Li ...
 
 
 
Molecular Biology
 
 
 
 
Zika virus non-coding RNAs antagonize antiviral responses by PKR-mediated translational arrest border= 
 
Horacio M Pallarés, María Mora González López Ledesma, Santiago Oviedo-Rouco, Luciana A Castellano, Guadalupe S Costa Navarro ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
Synergistic effect of split DNA activators of Cas12a with exon-unwinding and induced targeting effect border= 
 
Shen Huang, Yongliang Lou, Laibao Zheng
 
 
 
RTP801 interacts with the tRNA ligase complex and dysregulates its RNA ligase activity in Alzheimer's disease border= 
 
Genís Campoy-Campos, Julia Solana-Balaguer, Anna Guisado-Corcoll, Almudena Chicote-González, Pol Garcia-Segura ...
 
 
 
Making target sites in large structured RNAs accessible to RNA-cleaving DNAzymes through hybridization with synthetic DNA oligonucleotides border= 
 
Connor Nurmi, Jimmy Gu, Amal Mathai, John D Brennan, Yingfu Li
 
 
 
Accelerated discovery and miniaturization of novel single-stranded cytidine deaminases border= 
 
Jiacheng Deng, Xueyuan Li, Hao Yu, Lin Yang, Ziru Wang ...
 
 
 
RNA and RNA-protein complexes
 
 
 
 
Complete list of canonical post-transcriptional modifications in the Bacillus subtilis ribosome and their link to RbgA driven large subunit assembly border= 
 
Anna M Popova, Nikhil Jain, Xiyu Dong, Farshad Abdollah-Nia, Robert A Britton ...
 
 
 
Structural basis for a highly conserved RNA-mediated enteroviral genome replication border= 
 
Naba Krishna Das, Jeff Vogt, Alisha Patel, Hasan Al Banna, Deepak Koirala
 
 
 
Dynamics of diversified A-to-I editing in Streptococcus pyogenes is governed by changes in mRNA stability border= 
 
Thomas F Wulff, Karin Hahnke, Anne-Laure Lécrivain, Katja Schmidt, Rina Ahmed-Begrich ...
 
 
 
Assembly of the bacterial ribosome with circularly permuted rRNA border=  
 
Xiyu Dong, Kai Sheng, Luca F R Gebert, Sriram Aiyer, Ian J MacRae ...
 
 
 
LRPPRC and SLIRP synergize to maintain sufficient and orderly mammalian mitochondrial translation border= 
 
Diana Rubalcava-Gracia, Kristina Bubb, Fredrik Levander, Stephen P Burr, Amelie V August ...
 
 
 
Global analysis of the RNA'RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO border= 
 
Fergal J Hamrock, Daniel Ryan, Ali Shaibah, Anna S Ershova, Aalap Mogre ...
 
 
 
Structural Biology
 
 
 
 
Structural basis for difunctional mechanism of m-AMSA against African swine fever virus pP1192R border= 
 
Ruili Liu, Junqing Sun, Lian-Feng Li, Yingxian Cheng, Meilin Li ...
 
 
 
Structural basis of AUC codon discrimination during translation initiation in yeast border= 
 
Laura Villamayor-Belinchón, Prafful Sharma, Yuliya Gordiyenko, Jose L Llácer, Tanweer Hussain
 
 
 
Structural basis for the concerted antiphage activity in the SIR2'HerA system border=  
 
Fumeng Liao, Guimei Yu, Chendi Zhang, Zhikun Liu, Xuzichao Li ...
 
 
 
Structural basis of DNA recognition by BEN domain proteins reveals a role for oligomerization in unmethylated DNA selection by BANP border= 
 
Jiahao Ren, Junmeng Wang, Yanpeng Ren, Yuyang Zhang, Pengshuai Wei ...
 
 
 
Synthetic Biology and Bioengineering
 
 
 
 
Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules border= 
 
Jongoh Shin, Daniel C Zielinski, Bernhard O Palsson
 
 
 
CRISETR: an efficient technology for multiplexed refactoring of biosynthetic gene clusters border= 
 
Fuqiang He, Xinpeng Liu, Min Tang, Haiyi Wang, Yun Wu ...
 
 
 
Reconstruction of a robust bacterial replication module border=  
 
Tao Wang, Fan He, Ting He, Chen Lin, Xin Guan ...
 
 
 
Correction
 
 
 
 
Correction to ˜Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch' border= 
 
 
 
 
Correction to ˜Structural basis for difunctional mechanism of m-AMSA against African swine fever virus pP1192R' border= 
 
 
 
 
Correction to ˜Efficient circularization of protein-encoding RNAs via a novel cis-splicing system' border= 
 
 
 
 
Correction to ˜MRE11 UFMylation promotes ATM activation' border= 
 
 
 
 
Correction to ˜Advancing quantitative PCR with color cycle multiplex amplification' border= 
 
 
 
 
Correction to ˜Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria' border= 
 
 
 
 
Methods
 
 
 
 
Identification of transcription factor co-binding patterns with non-negative matrix factorization border= 
 
Ieva Rauluseviciute, Timothée Launay, Guido Barzaghi, Sarvesh Nikumbh, Boris Lenhard ...
 
 
 
Force-enhanced sensitive and specific detection of DNA-intercalative agents directly from microorganisms at single-molecule level border= 
 
Tianyu Liu, Teng Cai, Junfeng Huo, Hongwei Liu, Aiying Li ...
 
 
 
Learning to quantify uncertainty in off-target activity for CRISPR guide RNAs border=  
 
Furkan Özden, Peter Minary
 
 
 
DFF-ChIP: a method to detect and quantify complex interactions between RNA polymerase II, transcription factors, and chromatin border= 
 
Benjamin M Spector, Juan F Santana, Miles A Pufall, David H Price
 
 
 
DORQ-seq: high-throughput quantification of femtomol tRNA pools by combination of cDNA hybridization and Deep sequencing border= 
 
Kristen Marco, Lander Marc, Kilz Lea-Marie, Gleue Lukas, Jörg Marko ...
 
 
 
Using nucleolytic toxins as restriction enzymes enables new RNA applications border= 
 
Ulli Rothweiler, Sigurd Eidem Gundesø, Emma Wu Mikalsen, Steingrim Svenning, Mahavir Singh ...
 
 
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