Subject: Nucleic Acids Research Table of Contents for 11 November 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 20
 
11 November 2024
 
button-issue.png
 
 
NAR Breakthrough Article
 
 
 
 
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors border= 
 
Vladimir Mindel, Sagie Brodsky, Hadas Yung, Wajd Manadre, Naama Barkai
 
 
 
Critical Reviews and Perspectives
 
 
 
 
Re-appraising the evidence for the source, regulation and function of p53-family isoforms border= 
 
Ignacio López, Irene Larghero Valdivia, Borivoj Vojtesek, Robin Fåhraeus, Philip J Coates
 
 
 
What is the real value of omics data? Enhancing research outcomes and securing long-term data excellence border= 
 
Eva Price, Felix Feyertag, Thomas Evans, James Miskin, Kyriacos Mitrophanous ...
 
 
 
Chemical Biology and Nucleic Acid Chemistry
 
 
 
 
Development of hydrophobic tag purifying monophosphorylated RNA for chemical synthesis of capped mRNA and enzymatic synthesis of circular mRNA border= 
 
Mami Ototake, Masahito Inagaki, Seigo Kimura, Kaoru Onda, Mizuki Tada ...
 
 
 
SUPREM: an engineered non-site-specific m6 A RNA methyltransferase with highly improved efficiency border= 
 
Yoshiki Ochiai, Ben E Clifton, Madeleine Le Coz, Marco Terenzio, Paola Laurino
 
 
 
 
 
Computational Biology
 
 
 
 
Dual decoding of cell types and gene expression in spatial transcriptomics with PANDA border= 
 
Meng-Guo Wang, Luonan Chen, Xiao-Fei Zhang
 
 
 
Localization and discrimination of GG mismatch in duplex DNA by synthetic ligand-enhanced protein nanopore analysis border= 
 
Wenping Lyu, Jianji Zhu, XiaoQin Huang, Mauro Chinappi, Denis Garoli ...
 
 
 
Data Resources and Analyses
 
 
 
 
Revisiting the y-ome of Escherichia coli border= 
 
Lisa R Moore, Ron Caspi, Dana Boyd, Mehmet Berkmen, Amanda Mackie ...
 
 
 
Gene Regulation, Chromatin and Epigenetics
 
 
 
 
Establishment of closed 35S ribosomal RNA gene chromatin in stationary Saccharomyces cerevisiae cells border= 
 
Virginia Babl, Philipp Girke, Sebastian Kruse, Sophia Pinz, Katharina Hannig ...
 
 
 
Massively parallel binding assay (MPBA) reveals limited transcription factor binding cooperativity, challenging models of specificity border= 
 
Tamar Jana Lang, Sagie Brodsky, Wajd Manadre, Matan Vidavski, Gili Valinsky ...
 
 
 
 
PTBP1 mediates Sertoli cell actin cytoskeleton organization by regulating alternative splicing of actin regulators border= 
 
Yuexi Wang, Ullas Valiya Chembazhi, Danielle Yee, Sijie Chen, Jie Ji ...
 
 
 
Integrated multi-omics analysis of PBX1 in mouse adult neural stem- and progenitor cells identifies a transcriptional module that functionally links PBX1 to TCF3/4 border= 
 
Vera Laub, Elisabeth Nan, Lena Elias, Ian J Donaldson, Mette Bentsen ...
 
 
 
Core enhancers of the 3²RR optimize IgH nuclear position and loop conformation for successful oriented class switch recombination border= 
 
Charlotte Bruzeau, Ophélie Martin, Justine Pollet, Morgane Thomas, Zhaoqing Ba ...
 
 
 
Genome Integrity, Repair and Replication
 
 
 
 
Genome editing outcomes reveal mycobacterial NucS participates in a short-patch repair of DNA mismatches border= 
 
Tanjina Islam, Eric A Josephs
 
 
 
Mycobacterium smegmatis NucS-promoted DNA mismatch repair involves limited resection by a 5²-3² exonuclease and is independent of homologous recombination and NHEJ border= 
 
Iris V Rivera-Flores, Emily X Wang, Kenan C Murphy
 
 
 
DciA secures bidirectional replication initiation in Vibrio cholerae border= 
 
Amelie Besombes, Yazid Adam, Christophe Possoz, Ivan Junier, Francois-Xavier Barre ...
 
 
 
Switch-like phosphorylation of WRN integrates end-resection with RAD51 metabolism at collapsed replication forks border= 
 
Valentina Palermo, Eva Malacaria, Maurizio Semproni, Serena Camerini, Marialuisa Casella ...
 
 
 
p53-dependent crosstalk between DNA replication integrity and redox metabolism mediated through a NRF2-PARP1 axis border= 
 
Gamal Ahmed Elfar, Obed Aning, Tsz Wai Ngai, Pearlyn Yeo, Joel Wai Kit Chan ...
 
 
 
3,N4 -Etheno-5-methylcytosine blocks TET1-3 oxidation but is repaired by ALKBH2, 3 and FTO border= 
 
Jian Ma, Rui Qi, Emily M Harcourt, Yi-Tzai Chen, Giovannia M Barbosa ...
 
 
 
Disparate requirements for RAD54L in replication fork reversal border=  
 
Mollie E Uhrig, Neelam Sharma, Petey Maxwell, Jordi Gomez, Platon Selemenakis ...
 
 
 
Structural mechanisms of SLF1 interactions with Histone H4 and RAD18 at the stalled replication fork border= 
 
Emma L Ryder, Nazia Nasir, Amy E O Durgan, Michael Jenkyn-Bedford, Stephanie Tye ...
 
 
 
Human hnRNPA1 reorganizes telomere-bound replication protein A border=  
 
Sophie L Granger, Richa Sharma, Vikas Kaushik, Mortezaali Razzaghi, Masayoshi Honda ...
 
 
 
Pathological R-loops in bacteria from engineered expression of endogenous antisense RNAs whose synthesis is ordinarily terminated by Rho border= 
 
Apuratha Pandiyan, Jillella Mallikarjun, Himanshi Maheshwari, Jayaraman Gowrishankar
 
 
 
Haplotype-resolved de novo assembly revealed unique characteristics of alternative lengthening of telomeres in mouse embryonic stem cells border= 
 
Hyunji Lee, Hiroyuki Niida, Sanghyun Sung, Junho Lee
 
 
 
Altered dNTP pools accelerate tumor formation in mice border=  
 
Phong Tran, Pradeep Mishra, Leonard G Williams, Roman Moskalenko, Sushma Sharma ...
 
 
 
N2 -Alkyl-dG lesions elicit R-loop accumulation in the genome border= 
 
Yinan Wang, Feng Tang, Ting Zhao, Jun Yuan, Andrew H Kellum, Jr. ...
 
 
 
Genomics
 
 
 
 
Pipolins are bimodular platforms that maintain a reservoir of defense systems exchangeable with various bacterial genetic mobile elements border= 
 
Víctor Mateo-Cáceres, Modesto Redrejo-Rodríguez
 
 
 
Molecular and Structural Biology
 
 
 
 
The Swi5'Sfr1 complex regulates Dmc1- and Rad51-driven DNA strand exchange proceeding through two distinct three-stranded intermediates by different mechanisms border= 
 
Kentaro Ito, Takahisa Maki, Shuji Kanamaru, Masayuki Takahashi, Hiroshi Iwasaki
 
 
 
Ribosome Quality Control mitigates the cytotoxicity of ribosome collisions induced by 5-Fluorouracil border= 
 
Susanta Chatterjee, Parisa Naeli, Okan Onar, Nicole Simms, Aitor Garzia ...
 
 
 
Selective degradation of phage RNAs by the Csm6 ribonuclease provides robust type III CRISPR immunity in Streptococcus thermophilus border= 
 
Katie A Johnson, Sandra C Garrett, Christopher Noble-Molnar, Hanna A Elgarhi, Walter T Woodside ...
 
 
 
Chromosomal integrons are genetically and functionally isolated units of genomes border= 
 
Paula Blanco, Filipa Trigo da Roza, Laura Toribio-Celestino, Lucía García-Pastor, Niccolò Caselli ...
 
 
 
Self-assembly and condensation of intermolecular poly(UG) RNA quadruplexes border=  
 
Saeed Roschdi, Eric J Montemayor, Rahul Vivek, Craig A Bingman, Samuel E Butcher
 
 
 
Molecular Biology
 
 
 
 
Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication border= 
 
Mariana Sanchez-Londono, Selina Rust, Rogelio Hernández-Tamayo, José Vicente Gomes-Filho, Martin Thanbichler ...
 
 
 
Nucleic Acid Enzymes
 
 
 
 
Probing the mechanism of nick searching by LIG1 at the single-molecule level border= 
 
Surajit Chatterjee, Loïc Chaubet, Aafke van den Berg, Ann Mukhortava, Danah Almohdar ...
 
 
 
Structure-based discovery of first inhibitors targeting the helicase activity of human PIF1 border= 
 
Mark J A Wever, Francesca R Scommegna, Sara Egea-Rodriguez, Saba Dehghani-Tafti, Jose Brandao-Neto ...
 
 
 
RNA and RNA-protein complexes
 
 
 
 
TIRR regulates mRNA export and association with P-bodies in response to DNA damage border= 
 
Michelle S Glossop, Irina Chelysheva, Ruth F Ketley, Adele Alagia, Monika Gullerova
 
 
 
Evolving Escherichia coli to use a tRNA with a non-canonical fold as an adaptor of the genetic code border= 
 
Martin P Edelmann, Sietse Couperus, Emilio Rodríguez-Robles, Julie Rivollier, Tania M Roberts ...
 
 
 
The TRIM-NHL RNA-binding protein Brain Tumor coordinately regulates expression of the glycolytic pathway and vacuolar ATPase complex 
 
Robert P Connacher, Richard T Roden, Kai-Lieh Huang, Amanda J Korte, Saathvika Yeruva ...
 
 
 
The interplay between peptides and RNA is critical for protoribosome compartmentalization and stability border= 
 
Simone Codispoti, Tomoko Yamaguchi, Mikhail Makarov, Valerio G Giacobelli, Martin Mašek ...
 
 
 
Protein'RNA interactions mediated by silvestrol'insight into a unique molecular clamp border= 
 
Sai Kiran Naineni, Garvit Bhatt, Ekkanat Jiramongkolsiri, Francis Robert, Regina Cencic ...
 
 
 
Phylogenomic instructed target analysis reveals ELAV complex binding to multiple optimally spaced U-rich motifs border= 
 
David W J McQuarrie, Matthias Soller
 
 
 
Structural Biology
 
 
 
 
Molecular basis for the transcriptional regulation of an epoxide-based virulence circuit in Pseudomonas aeruginosa 
 
Susu He, Noor M Taher, Adam R Simard, Kelli L Hvorecny, Michael J Ragusa ...
 
 
 
Structural and functional insights into the interaction between the bacteriophage T4 DNA processing proteins gp32 and Dda border= 
 
Xiaoping He, Mi-Kyung Yun, Zhenmei Li, M Brett Waddell, Amanda Nourse ...
 
 
 
Corrections
 
 
 
 
Correction to ˜CRISPR perfect adaptation for robust control of cellular immune and apoptotic responses' border= 
 
 
 
 
Correction to ˜DORQ-seq: high-throughput quantification of femtomol tRNA pools by combination of cDNA hybridization and Deep sequencing' border= 
 
 
 
 
Correction to ˜Accelerated discovery and miniaturization of novel single-stranded cytidine deaminases' border= 
 
 
 
 
Methods
 
 
 
 
Nuclease-induced stepwise photodropping (NISP) to precisely investigate single-stranded DNA degradation behaviors of exonucleases and endonucleases border=  
 
Hui-Pin Chiu, Chung-Han Shen, Jan-Kai Wu, Eric Y C Mao, Han-Yi Yen ...
 
 
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.mcmaster.ca.