Works matching IS 03051048 AND DT 2025 AND VI 53 AND IP 7

Results: 50

CRISPR RNA binding drives structural ordering that primes Cas7-11 for target cleavage Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf271

By:

Lin, Calvin P;
Li, Harry;
Brogan, Daniel J;
Wang, Tianqi;
Akbari, Omar S;
Komives, Elizabeth A

Publication type:

Article

The ZBTB24-CDCA7-HELLS axis suppresses the totipotent 2C-like reprogramming by maintaining Dux methylation and repression Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf302

By:

Guo, Dan;
Du, Zeling;
Liu, Youqi;
Lin, Meiqi;
Lu, Yue;
Hardikar, Swanand;
Xue, Yanna;
Zhang, Jinghong;
Chen, Taiping;
Dan, Jiameng

Publication type:

Article

Proteome-wide microarray-based screening of PAR-binding proteins Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf300

By:

Gu Kang, Bong;
Kang, Sung-Ung;
Jin Kim, Jae;
Kwon, Ji-Sun;
Gagné, Jean-Philippe;
Yun Lee, Seo;
Kim, Soyeon;
Lee, Karl S;
Ha, Shinwon;
Seop Jeong, Jun;
Lee, Yun-Il;
Zhu, Heng;
Kim, Dongsan;
Poirier, Guy G;
Chul Kang, Ho;
Dawson, Valina L;
Dawson, Ted M

Publication type:

Article

Naphthalene diimide-naphthalimide dyads promote telomere damage by selectively targeting multimeric G-quadruplexes Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf301

By:

Pirota, Valentina;
Iachettini, Sara;
Platella, Chiara;
Zizza, Pasquale;
Fracchioni, Giorgia;
Di Vito, Serena;
Carachino, Alice;
Battistini, Federica;
Orozco, Modesto;
Freccero, Mauro;
Biroccio, Annamaria;
Montesarchio, Daniela;
Doria, Filippo

Publication type:

Article

SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf320

By:

Zhang, Ren-Gang;
Shang, Hong-Yun;
Milne, Richard Ian;
Almeida-Silva, Fabricio;
Chen, Hengchi;
Zhou, Min-Jie;
Shu, Heng;
Jia, Kai-Hua;
Van de Peer, Yves;
Ma, Yong-Peng

Publication type:

Article

NicOPURE: nickless RNA circularization and one-step purification with engineered group II introns and cyclizing UTRs Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf310

By:

Gao, Xiang;
Chen, Kelei;
Wang, Honglei

Publication type:

Article

High-resolution mapping of sigma factor DNA-binding sequences using artificial promoters, RNA aptamers, and deep sequencing Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf306

By:

Khan, Essa Ahsan;
Rückert-Reed, Christian;
Dahiya, Gurvinder Singh;
Tietze, Lisa;
Fages-Lartaud, Maxime;
Busche, Tobias;
Kalinowski, Jörn;
Shingler, Victoria;
Lale, Rahmi

Publication type:

Article

Rapid discovery of functional RNA domains Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf307

By:

Latifi, Brandon;
Cole, Kyle H;
Vu, Michael M K;
Lupták, Andrej

Publication type:

Article

Deciphering the biosynthetic potential of microbial genomes using a BGC language processing neural network model Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf305

By:

Lai, Qilong;
Yao, Shuai;
Zha, Yuguo;
Zhang, Haohong;
Zhang, Haobo;
Ye, Ying;
Zhang, Yonghui;
Bai, Hong;
Ning, Kang

Publication type:

Article

Benchmarking computational methods for detecting spatial domains and domain-specific spatially variable genes from spatial transcriptomics data Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf303

By:

Kang, Liping;
Zhang, Qinglong;
Qian, Fan;
Liang, Junyao;
Wu, Xiaohui

Publication type:

Article

Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf297

By:

Wilson, Thomas Stuart;
Noberini, Roberta;
Moysidou, Eirini;
Ojukwu, Ifeyinwa;
Milan, Marta;
Jiang, Ming;
Kelly, Gavin;
Howell, Michael;
Bonaldi, Tiziana;
Scaffidi, Paola

Publication type:

Article

Molecular basis for RNA discrimination by human DNA ligase 1 Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf299

By:

Tumbale, Percy P;
Jurkiw, Thomas J;
Krahn, Juno M;
Bokil, Neha V;
Admiraal, Suzanne J;
Pedersen, Lars C;
Williams, Jessica S;
Kunkel, Tom A;
O'Brien, Patrick J;
Williams, R Scott

Publication type:

Article

Oxidative stress at telomeres triggers internal DNA loops, TRF1 dissociation, and TRF2-dependent R-loops Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf285

By:

Nguyen, Trang Thu;
Mazzucco, Giulia;
Kyriacou, Eftychia;
Lunardi, Thomas;
Brandl, Leona;
Ahmed, Wareed;
Doksani, Ylli;
Lingner, Joachim

Publication type:

Article

Non-canonical DNA in human and other ape telomere-to-telomere genomes Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf298

By:

Smeds, Linnéa;
Kamali, Kaivan;
Kejnovská, Iva;
Kejnovský, Eduard;
Chiaromonte, Francesca;
Makova, Kateryna D

Publication type:

Article

Tailoring and reversing m<sup>6</sup>A editing with sequential RNA bioorthogonal chemistry Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf283

By:

Liu, Xingyu;
Qi, Qianqian;
Xiong, Wei;
Zhang, Yuanyuan;
Shen, Wei;
Xu, Xinyan;
Zhao, Yunting;
Li, Ming;
Zhou, Enyi;
Tian, Tian;
Zhou, Xiang

Publication type:

Article

Selict-seq profiles genome-wide off-target effects in adenosine base editing Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf281

By:

Yuan, Kexin;
Xi, Xin;
Han, Shaoqing;
Han, Jingyu;
Zhao, Bin;
Wei, Qi;
Zhou, Xiang

Publication type:

Article

Activation, incompatibility, and displacement of FIB replicons in E. coliOpen Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf275

By:

Lloyd, Georgina S;
Stephens, Elton R;
Di Maio, Alessandro;
Thomas, Christopher M

Publication type:

Article

tRNA binding to Kti12 is crucial for wobble uridine modification by Elongator Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf296

By:

Scherf, David;
Hammermeister, Alexander;
Böhnert, Pauline;
Burkard, Alicia;
Helm, Mark;
Glatt, Sebastian;
Schaffrath, Raffael

Publication type:

Article

Cell-cycle dependence of bursty gene expression: insights from fitting mechanistic models to single-cell RNA-seq data Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf295

By:

Sukys, Augustinas;
Grima, Ramon

Publication type:

Article

Chromatin-associated α-satellite RNA maintains chromosome stability by reestablishing SAF-A in the mitotic cell cycle Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf294

By:

Ren, Bingbing;
Zhong, Yinchun;
Yang, Yan;
Chang, Shuhui;
Li, Yalun;
You, Mengzhen;
Shan, Ge;
Wang, Xueren;
Chen, Enguo

Publication type:

Article

Decoding the complex journeys of RNAs along neurons Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf293

By:

Wingfield, Jenna L;
Puthanveettil, Sathyanarayanan V

Publication type:

Article

Cryo-EM structures of DNA-free and DNA-bound BsaXI: architecture of a Type IIB restriction–modification enzyme Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf291

By:

Shen, Betty W;
Heiter, Dan;
Yang, Weiwei;
Xu, Shuang-yong;
Stoddard, Barry L

Publication type:

Article

Investigating the interplay between RNA structural dynamics and RNA chemical probing experiments Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf290

By:

Arnold, Ethan B;
Cohn, Daniel;
Bose, Emma;
Klingler, David;
Wolfe, Gregory;
Jones, Alisha N

Publication type:

Article

pC-SAC: A method for high-resolution 3D genome reconstruction from low-resolution Hi-C data Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf289

By:

Angel, J Carlos;
El Amraoui, Narjis;
Gürsoy, Gamze

Publication type:

Article

Maternal histone mRNAs are uniquely processed through polyadenylation in a Stem-Loop Binding Protein (SLBP) dependent manner Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf288

By:

Pérez-Roldán, Juan;
Henn, László;
Bernués, Jordi;
Torras-LLort, Mònica;
Tamirisa, Srividya;
Belloc, Eulàlia;
Rodríguez-Muñoz, Laura;
Timinszky, Gyula;
Jiménez, Gerardo;
Méndez, Raúl;
Carbonell, Albert;
Azorín, Fernando

Publication type:

Article

Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf287

By:

Liu, Qiong;
Jiang, Zhou;
Li, Sheng;
Li, Yinfeng;
Wan, Yingfei;
Hu, Zhenyu;
Ma, Shimeng;
Zou, Zhen;
Yang, Ronghua

Publication type:

Article

The linker region of a development-specific DNA polymerase X ensures efficient repair of programmed DNA double-strand breaks in Paramecium tetraureliaOpen Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf286

By:

Verron, Baptiste;
Arnaiz, Olivier;
Zangarelli, Coralie;
Mathy, Nathalie;
Bétermier, Mireille;
Bischerour, Julien

Publication type:

Article

UV induces codirectional replication–transcription conflicts and an alternative DnaA-dependent replication origin in the rnhAB mutants of EscherichiacoliOpen Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf282

By:

Kouzminova, Elena A;
Cronan, Glen E;
Kuzminov, Andrei

Publication type:

Article

Transcriptional induction by ecdysone in Drosophila salivary glands involves an increase in chromatin accessibility and acetylation Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf284

By:

Evdokimova, Aleksandra A;
Kolesnikova, Tatyana D;
Mazina, Marina Yu;
Krasnov, Aleksey N;
Erokhin, Maksim;
Chetverina, Darya;
Vorobyeva, Nadezhda E

Publication type:

Article

A specific pluripotency-associated eRNA controls Nanog locus by shaping the epigenetic landscape and stabilizing enhancer–promoter interaction Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf274

By:

Cuomo, Mariella;
Costabile, Davide;
Della Monica, Rosa;
Buonaiuto, Michela;
Trio, Federica;
De Riso, Giulia;
Visconti, Roberta;
Chiariotti, Lorenzo

Publication type:

Article

Structure of the nucleosome-bound human BCL7A Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf273

By:

Martin, Franck;
Kazrani, Asgar Abbas;
Lafouge, Julie;
Diaz-Jimenez, Dana Mariel;
Siebert, Stéphanie;
Fabbro-Burtschell, Leonie;
Maillard, Emma;
Lapouge, Karine;
Mertens, Haydyn David Thomas;
Sauter, Claude;
Leitner, Alexander;
Ochsenbein, Françoise;
Blais, Alexandre;
Bergamin, Elisa

Publication type:

Article

Nuclear actin-dependent Meg3 expression suppresses metabolic genes by affecting the chromatin architecture at sites of elevated H3K27 acetylation levels Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf280

By:

Hosny El Said, Nadine;
Abdrabou, Wael;
Mahmood, Syed Raza;
Venit, Tomas;
Idaghdour, Youssef;
Percipalle, Piergiorgio

Publication type:

Article

The PIN1–p38–CtIP signalling axis protects stalled replication forks from deleterious degradation Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf278

By:

Vivalda, Francesca;
Gatti, Marco;
Manfredi, Letizia;
Dogan, Hülya;
Porro, Antonio;
Collotta, Giulio;
Ceppi, Ilaria;
von Aesch, Christine;
van Ackeren, Vanessa;
Wild, Sebastian;
Steger, Martin;
Canovas, Begoña;
Cubillos-Rojas, Monica;
Riera, Antoni;
Cejka, Petr;
Nebreda, Angel R;
Dibitetto, Diego;
Rottenberg, Sven;
Sartori, Alessandro A

Publication type:

Article

De novo RNA base editing in plant organelles with engineered synthetic P-type PPR editing factors Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf279

By:

Mathieu, Sébastien;
Lesch, Elena;
Garcia, Shahinez;
Graindorge, Stéfanie;
Schallenberg-Rüdinger, Mareike;
Hammani, Kamel

Publication type:

Article

A two-step regulatory mechanism dynamically controls histone H3 acetylation by SAGA complex at growth-related promoters Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf276

By:

Zencir, Sevil;
Dilg, Daniel;
Bruzzone, Maria Jessica;
Stutz, Françoise;
Soudet, Julien;
Shore, David;
Albert, Benjamin

Publication type:

Article

Analysis of RNA translation with a deep learning architecture provides new insight into translation control Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf277

By:

Fan, Xiaojuan;
Chang, Tiangen;
Chen, Chuyun;
Hafner, Markus;
Wang, Zefeng

Publication type:

Article

LIET model: capturing the kinetics of RNA polymerase from loading to termination Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf246

By:

Stanley, Jacob T;
Barone, Georgia E F;
Townsend, Hope A;
Sigauke, Rutendo F;
Allen, Mary A;
Dowell, Robin D

Publication type:

Article

Poly-(ADP-ribose) serves as a scaffold for the methyltransferase METTL3/14 complex in the DNA damage response Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf244

By:

Gonzalez-Leal, Claudia;
Cai, Jin;
de Groot, Bram A F J;
Wegerer, Andreas;
Preisser, Julia;
Luijsterburg, Martijn S;
Ladurner, Andreas G

Publication type:

Article

Nucleotide-level characterization and improvement of l-arabinose- and l-rhamnose-inducible systems in E. coli using a high-throughput approach Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf224

By:

Kim, Nancy M;
Peng, Danqia;
Sandoval, Nicholas R

Publication type:

Article

Single-stranded DNA drives σ subunit loading onto mycobacterial RNA polymerase to unlock initiation-competent conformations Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf272

By:

Vishwakarma, Rishi Kishore;
Marechal, Nils;
Morichaud, Zakia;
Blaise, Mickaël;
Margeat, Emmanuel;
Brodolin, Konstantin

Publication type:

Article

The yeast CST and Polα/primase complexes act in concert to ensure proper telomere maintenance and protection Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf245

By:

Calugaru, Kimberly;
Yu, Eun Young;
Huang, Sophie;
González-Rodríguez, Nayim;
Coloma, Javier;
Lue, Neal F

Publication type:

Article

Conjugation to a transferrin receptor 1-binding Bicycle peptide enhances ASO and siRNA potency in skeletal and cardiac muscles Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf270

By:

Østergaard, Michael E;
Carrer, Michele;
Anderson, Brooke A;
Afetian, Megan;
Bakooshli, Mohsen A;
Santos, Jinro A;
Klein, Stephanie K;
Capitanio, Juliana;
Freestone, Graeme C;
Tanowitz, Michael;
Galindo-Murillo, Rodrigo;
Gaus, Hans J;
Dwyer, Chrissa A;
Jackson, Michaela;
Jafar-nejad, Paymaan;
Rigo, Frank;
Seth, Punit P;
Gaynor, Katherine U;
Stanway, Steven J;
Urbonas, Liudvikas

Publication type:

Article

Nuclear AGO2 supports influenza A virus replication through type-I interferon regulation Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf268

By:

Huang, Hsiang-Chi;
Fong, Michelle;
Nowak, Iwona;
Shcherbinina, Evgeniia;
Lobo, Vivian;
Besavilla, Danica F;
Huynh, Hang T;
Schön, Karin;
Westholm, Jakub O;
Fernandez, Carola;
Patel, Angana A H;
Wiel, Clotilde;
Sayin, Volkan I;
Anastasakis, Dimitrios G;
Angeletti, Davide;
Sarshad, Aishe A

Publication type:

Article

DuplexDiscoverer: a computational method for the analysis of experimental duplex RNA–RNA interaction data Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf266

By:

Semenchenko, Egor;
Tsybulskyi, Volodymyr;
Meyer, Irmtraud M

Publication type:

Article

Autophagy induction enhances homologous recombination-associated CRISPR–Cas9 gene editing Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf258

By:

Nam, Hye Jin;
Han, Jun Hee;
Yu, Jihyeon;
Cho, Chang Sik;
Kim, Dongha;
Kim, Young Eun;
Kim, Min Ji;
Kim, Jeong Hun;
Jo, Dong Hyun;
Bae, Sangsu

Publication type:

Article

Impacts of sequence and structure on pyrrolocytosine fluorescence in RNA Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf262

By:

Coulson, Taylor L;
Widom, Julia R

Publication type:

Article

Nutrient starvation-induced Hda1C rewiring: coordinated regulation of transcription and translation Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf256

By:

Lee, Min Kyung;
Kang, Byunghee;
Shin, Min-Kyung;
Kim, Yoon Ki;
Kim, Hye Young;
Lee, Soo Young;
Roh, Tae-Young;
Kim, TaeSoo

Publication type:

Article

High-throughput screen of 100 000 small molecules in C9ORF72 ALS neurons identifies spliceosome modulators that mobilize G4C2 repeat RNA into nuclear export and repeat associated non-canonical translation Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf253

By:

Luteijn, Maartje J;
Bhaskar, Varun;
Trojer, Dominic;
Schürz, Melanie;
Mahboubi, Hicham;
Handl, Cornelia;
Pizzato, Nicolas;
Pfeifer, Martin;
Dafinca, Ruxandra;
Voshol, Hans;
Giorgetti, Elisa;
Manneville, Carole;
Garnier, Isabelle P M;
Müller, Matthias;
Zeng, Fanning;
Buntin, Kathrin;
Markwalder, Roger;
Schröder, Harald;
Weiler, Jan;
Khar, Dora

Publication type:

Article

Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf255

By:

Fiorentino, Federica;
Thoms, Matthias;
Wild, Klemens;
Denk, Timo;
Cheng, Jingdong;
Zeman, Jakub;
Sinning, Irmgard;
Hurt, Ed;
Beckmann, Roland

Publication type:

Article

Light-controlled Spo11-less meiotic DNA breaks by MagTAQing lead to chromosomal aberrations Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 7, p. 1, doi. 10.1093/nar/gkaf206

By:

Yone, Hideyuki;
Kawashima, Yuri;
Hirai, Hayato;
Oda, Arisa H;
Sato, Moritoshi;
Kono, Hiromitsu;
Ohta, Kunihiro

Publication type:

Article