Works matching IS 03051048 AND DT 2025 AND VI 53 AND IP 4

Results: 78

Rescuing DNMT1 fails to fully reverse the molecular and functional repercussions of its loss in mouse embryonic stem cells.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf130

By:

Elder, Elizabeth;
Lemieux, Anthony;
Legault, Lisa-Marie;
Caron, Maxime;
Bertrand-Lehouillier, Virginie;
Dupas, Thomas;
Raynal, Noël J-M;
Bourque, Guillaume;
Sinnett, Daniel;
Gévry, Nicolas;
McGraw, Serge

Publication type:

Article

Correction to 'Recruitment of homodimeric proneural factors by conserved CAT–CAT E-boxes drives major epigenetic reconfiguration in cortical neurogenesis'.

Published in:: 2025
Publication type:: Correction Notice

Dynamics and evolutionary conservation of B complex protein recruitment during spliceosome activation.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf124

By:

Fu, Xingyang;
Hoskins, Aaron A

Publication type:

Article

Protein bL38 facilitates incorporation of uL6 during assembly of the 50S subunit in Flavobacterium johnsoniae.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf120

By:

Alom, Md Siddik;
Arpin, Dominic;
Zhu, Haojun;
Hay, Brenna N;
Foster, Leonard J;
Ortega, Joaquin;
Fredrick, Kurt

Publication type:

Article

Structural insights into human PNPase in health and disease.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf119

By:

Li, Yi-Ching;
Wang, Chun-Hsiung;
Patra, Malay;
Chen, Yi-Ping;
Yang, Wei-Zen;
Yuan, Hanna S

Publication type:

Article

Regulation of CRISPR trans-cleavage activity by an overhanging activator.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf117

By:

Yin, Na;
Yu, Hongyan;
Zhang, Li;
Luo, Fei;
Wang, Weitao;
Han, Xiaole;
He, Yu;
Zhang, Yiqi;
Wu, You;
Pu, Jiu;
Feng, Tong;
Yang, Gang;
Chen, Tingmei;
Xie, Guoming

Publication type:

Article

Virus-derived siRNA: Coronavirus and influenza virus trigger antiviral RNAi immunity in birds.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf116

By:

Wu, Yaotang;
Liu, Peng;
Zhou, Jie;
Fu, Mei;
Wang, Chenlu;
Xiong, Ningna;
Ji, Wenxin;
Wang, Zhisheng;
Lin, Jian;
Yang, Qian

Publication type:

Article

Evolving a terminal deoxynucleotidyl transferase for commercial enzymatic DNA synthesis.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf115

By:

Forget, Stephanie M;
Krawczyk, Mikayla J;
Knight, Anders M;
Ching, Charlene;
Copeland, Rachelle A;
Mahmoodi, Niusha;
Mayo, Melissa A;
Nguyen, James;
Tan, Amanda;
Miller, Mathew;
Vroom, Jonathan;
Lutz, Stefan

Publication type:

Article

Structure of the tilapia lake virus nucleoprotein bound to RNA.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf112

By:

Arragain, Benoît;
Pelosse, Martin;
Huard, Karine;
Cusack, Stephen

Publication type:

Article

DNA replication dynamics are associated with genome composition in Plasmodium species.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf111

By:

Totañes, Francis Isidore Garcia;
Chapman, Sarah E;
Rai, Subash Kumar;
Jones, Mathew J K;
Boemo, Michael A;
Merrick, Catherine J

Publication type:

Article

Structural basis of ssDNA-guided NADase activation of prokaryotic SPARTA system.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf110

By:

Hu, Rong;
Guo, Chenmin;
Liu, Xiaotian;
Lin, Yuanyi;
Yang, Zixin;
Li, Zhixin;
Yang, Ye;
Ma, Erman;
Li, Yiyi;
Chen, Jiyun;
Liu, Liang

Publication type:

Article

Transcription-replication conflicts drive R-loop-dependent nucleosome eviction and require DOT1L activity for transcription recovery.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf109

By:

Werner, Marcel;
Trauner, Manuel;
Schauer, Tamas;
Ummethum, Henning;
Márquez-Gómez, Elizabeth;
Lalonde, Maxime;
Lee, Clare S K;
Tsirkas, Ioannis;
Sajid, Atiqa;
Murriello, Augusto C;
Längst, Gernot;
Hamperl, Stephan

Publication type:

Article

The NEXT complex regulates H3K27me3 levels to affect cancer progression by degrading G4/U-rich lncRNAs.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf107

By:

Yang, Qianqian;
Zhou, Zihan;
Li, Lian;
Lu, Runhui;
Hou, Guofang;
Huang, Caihu;
Huang, Jiayi;
Li, Hongyan;
Zhang, Yafan;
Li, Junya;
Zhang, Yixin;
Xu, Anan;
Chen, Ran;
Wang, Yanli;
Zhao, Xian;
Huang, Jian;
Wang, Yiwei;
Zhao, Xiaojing;
Yu, Jianxiu

Publication type:

Article

Shiba: a versatile computational method for systematic identification of differential RNA splicing across platforms.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf098

By:

Kubota, Naoto;
Chen, Liang;
Zheng, Sika

Publication type:

Article

Disassembly of unstable RNA structures by an E. coli DEAD-box chaperone accelerates ribosome assembly.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf104

By:

Sun, Yunsheng;
Woodson, Sarah A

Publication type:

Article

Structural basis of endo-siRNA processing by Drosophila Dicer-2 and Loqs-PD.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf102

By:

Cao, Na;
Wang, Jia;
Deng, Ting;
Fan, Boming;
Su, Shichen;
Ma, Jinbiao;
Wang, Hong-Wei

Publication type:

Article

Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf101

By:

Chovanec, Peter;
Yin, Yi

Publication type:

Article

Correction to 'A modular toolbox for the optogenetic deactivation of transcription'.

Published in:: 2025
Publication type:: Correction Notice

Phosphorylated BLM peptide acts as an agonist for DNA damage response.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf106

By:

Agrawal, Ritu;
Agarwal, Himanshi;
Mukherjee, Chetana;
Chakraborty, Baishali;
Sharma, Vandana;
Tripathi, Vivek;
Kumar, Nitin;
Priya, Swati;
Gupta, Nidhi;
Jhingan, Gagan Deep;
Bajaj, Avinash;
Sengupta, Sagar

Publication type:

Article

Sequence-dependent and -independent effects of intron-mediated enhancement learned from thousands of random introns.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf097

By:

Kowal, Emma J K;
Sakai, Yuta;
McGurk, Michael P;
Pasetsky, Zoe J;
Burge, Christopher B

Publication type:

Article

Structures of the cyanobacterial nitrogen regulators NtcA and PipX complexed to DNA shed light on DNA binding by NtcA and implicate PipX in the recruitment of RNA polymerase.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf096

By:

Forcada-Nadal, Alicia;
Bibak, Sirine;
Salinas, Paloma;
Contreras, Asunción;
Rubio, Vicente;
Llácer, José L

Publication type:

Article

Crossovers are regulated by a conserved and disordered synaptonemal complex domain.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf095

By:

Neves, Ana Rita Rodrigues;
Čavka, Ivana;
Rausch, Tobias;
Köhler, Simone

Publication type:

Article

The structure of the MutL-CTD:processivity-clamp complex provides insight regarding strand discrimination in non-methyl-directed DNA mismatch repair.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf094

By:

Nirwal, Shivlee;
Jha, Ritika;
Narayanan, Naveen;
Sharma, Minakshi;
Kulkarni, Dhananjaya S;
Sharma, Dalchand;
Babu, Amith S;
Suthar, Dhiraj K;
Rao, Desirazu N;
Nair, Deepak T

Publication type:

Article

The lncRNA DUBR is regulated by CTCF and coordinates chromatin landscape and gene expression in hematopoietic cells.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf093

By:

Núñez-Martínez, Hober Nelson;
Tapia-Urzúa, Gustavo;
Cerecedo-Castillo, Ángel Josué;
Peralta-Alvarez, Carlos Alberto;
Guerrero, Georgina;
Huarte, Maite;
Recillas-Targa, Félix

Publication type:

Article

Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf092

By:

Liu, Lingjie;
Zhao, Yixin;
Hassett, Rebecca;
Toneyan, Shushan;
Koo, Peter K;
Siepel, Adam

Publication type:

Article

paraCell: a novel software tool for the interactive analysis and visualization of standard and dual host–parasite single-cell RNA-seq data.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf091

By:

Agboraw, Edward;
Haese-Hill, William;
Hentzschel, Franziska;
Briggs, Emma;
Aghabi, Dana;
Heawood, Anna;
Harding, Clare R;
Shiels, Brian;
Crouch, Kathryn;
Somma, Domenico;
Otto, Thomas D

Publication type:

Article

Global chromatin reorganization and regulation of genes with specific evolutionary ages during differentiation and cancer.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf084

By:

Raynal, Flavien;
Sengupta, Kaustav;
Plewczynski, Dariusz;
Aliaga, Benoît;
Pancaldi, Vera

Publication type:

Article

NAIL-MS reveals tRNA and rRNA hypomodification as a consequence of 5-fluorouracil treatment.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf090

By:

Berg, Maximilian;
Li, Chengkang;
Kaiser, Stefanie

Publication type:

Article

RNA exosome-driven RNA processing instructs the duration of the unfolded protein response.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf088

By:

Matabishi-Bibi, Laura;
Goncalves, Coralie;
Babour, Anna

Publication type:

Article

Precise gene expression deconvolution in spatial transcriptomics with STged.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf087

By:

Tu, Jia-Juan;
Yan, Hong;
Zhang, Xiao-Fei;
Lin, Zhixiang

Publication type:

Article

XRCC1 mediates PARP1- and PAR-dependent recruitment of PARP2 to DNA damage sites.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf086

By:

Lin, Xiaohui;
Leung, Kay Sze Karina;
Wolfe, Kaitlynn F;
Call, Nicolas;
Bhandari, Seema Khattri;
Huang, Xiaoyu;
Lee, Brian J;
Tomkinson, Alan E;
Zha, Shan

Publication type:

Article

The G-quadruplex experimental drug QN-302 impairs liposarcoma cell growth by inhibiting MDM2 expression and restoring p53 levels.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf085

By:

Tosoni, Beatrice;
Naghshineh, Eisa;
Zanin, Irene;
Gallina, Irene;
Di Pietro, Lorenzo;
Cleris, Loredana;
Nadai, Matteo;
Lecchi, Mara;
Verderio, Paolo;
Pratesi, Pietro;
Pasquali, Sandro;
Zaffaroni, Nadia;
Neidle, Stephen;
Folini, Marco;
Richter, Sara N

Publication type:

Article

Characterization of group I introns in generating circular RNAs as vaccines.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf089

By:

Liao, Kuo-Chieh;
Eshaghi, Majid;
Hong, Zebin;
Saw, Tzuen Yih;
Lim, Jian An Jovi;
Han, Jian;
Aw, Jong Ghut Ashley;
Tan, Kiat Yee;
Yap, Aixin;
Gao, Xiang;
Cheng, Youzhi Anthony;
Lim, Su Ying;
Cheang, You Zhi Nicholas;
Saron, Wilfried A A;
Rathore, Abhay P S;
Zhang, Li;
Shunmuganathan, Bhuvaneshwari;
Gupta, Rashi;
Tan, Siang Ling Isabelle;
Qian, Xinlei

Publication type:

Article

Oncohistone H3 E97K mutation facilitates CENP-A mislocalization and chromosomal instability in budding yeast.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf083

By:

Ohkuni, Kentaro;
Au, Wei-Chun;
Kazi, Amira Z;
Balachandra, Vinutha;
Basrai, Munira A

Publication type:

Article

Strategic base modifications refine RNA function and reduce CRISPR–Cas9 off-targets.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf082

By:

Zhang, Kaisong;
Shen, Wei;
Zhao, Yunting;
Xu, Xinyan;
Liu, Xingyu;
Qi, Qianqian;
Huang, Siqi;
Tian, Tian;
Zhou, Xiang

Publication type:

Article

Multifaceted roles of H2B mono-ubiquitylation in D-loop metabolism during homologous recombination repair.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf081

By:

Hung, Shih-Hsun;
Liang, Yuan;
Heyer, Wolf-Dietrich

Publication type:

Article

Inter-domain communication in the dimeric DEAD-box helicase Hera from T. thermophilus and implications for the mechanism of RNA unwinding.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf080

By:

Donsbach, Pascal;
Kwas, Carolin;
Steimer, Lenz;
Samatanga, Brighton;
Andreou, Alexandra Z;
Klostermeier, Dagmar

Publication type:

Article

An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf079

By:

Wang, Yi-Hui;
Hertz, Hannah L;
Pastore, Benjamin;
Tang, Wen

Publication type:

Article

Cancer cell target discovery: comparing laboratory evolution of expanded DNA six-nucleotide alphabets with standard four-nucleotide alphabets.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf072

By:

Shaker, Sharpkate;
Li, Jun;
Wan, Shuo;
Xuan, Hong;
Long, Jinchen;
Cao, Haiyan;
Wei, Tongxuan;
Liu, Qinguo;
Xu, Da;
Benner, Steven A;
Zhang, Liqin

Publication type:

Article

Using minor variant genomes and machine learning to study the genome biology of SARS-CoV-2 over time.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf077

By:

Dong, Xiaofeng;
Matthews, David A;
Gallo, Giulia;
Darby, Alistair;
Donovan-Banfield, I'ah;
Goldswain, Hannah;
MacGill, Tracy;
Myers, Todd;
Orr, Robert;
Bailey, Dalan;
Carroll, Miles W;
Hiscox, Julian A

Publication type:

Article

Ubiquitin protease Ubp1 cooperates with Ubp10 and Ubp12 to revert lysine-164 PCNA ubiquitylation at replication forks.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf076

By:

Zamarreño, Javier;
Rodríguez, Sergio;
Muñoz, Sofía;
Bueno, Avelino;
Sacristán, María P

Publication type:

Article

A plasmid-encoded inactive toxin–antitoxin system MtvT/MtvA regulates plasmid conjugative transfer and bacterial virulence in Pseudomonas aeruginosa.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf075

By:

Li, Meng;
Guo, Hua;
Wang, Lecheng;
Tao, Ruixue;
Song, Gaoyu;
Cao, Linke;
Yan, Wenbo;
Wu, Ziyuan;
Liu, Qian;
Chen, Yaodong;
Gong, Lei;
Wang, Tietao;
Zhang, Yani

Publication type:

Article

NEAT1-mediated regulation of proteostasis and mRNA localization impacts autophagy dysregulation in Rett syndrome.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf074

By:

Siqueira, Edilene;
Velasco, Cecilia D;
Tarrasón, Ariadna;
Soler, Marta;
Srinivas, Tara;
Setién, Fernando;
Oliveira-Mateos, Cristina;
Casado-Pelaez, Marta;
Martinez-Verbo, Laura;
Armstrong, Judith;
Esteller, Manel;
Alves, Letícia F;
Llobet, Artur;
Guil, Sonia

Publication type:

Article

FuSViz—visualization and interpretation of structural variation using cancer genomics and transcriptomics data.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf078

By:

Zhao, Sen;
Nakken, Sigve;
Vodak, Daniel;
Hovig, Eivind

Publication type:

Article

The human genome encodes a multitude of novel miRNAs.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf070

By:

Gao, Fan;
Wang, Fang;
Chen, Yue;
Deng, Bolin;
Yang, Fujian;
Cao, Huifen;
Chen, Junjie;
Chen, Huiling;
Qi, Fei;
Kapranov, Philipp

Publication type:

Article

Discovery of reversing enzymes for RNA ADP-ribosylation reveals a possible defence module against toxic attack.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf069

By:

Lu, Yang;
Schuller, Marion;
Bullen, Nathan P;
Mikolcevic, Petra;
Zonjic, Iva;
Raggiaschi, Roberto;
Mikoc, Andreja;
Whitney, John C;
Ahel, Ivan

Publication type:

Article

DHX9 helicase impacts on splicing decisions by modulating U2 snRNP recruitment in Ewing sarcoma cells.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf068

By:

Frezza, Valentina;
Chellini, Lidia;
Riccioni, Veronica;
Bonvissuto, Davide;
Palombo, Ramona;
Paronetto, Maria Paola

Publication type:

Article

Oxidative damage within alternative DNA structures results in aberrant mutagenic processing.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf066

By:

Zewail-Foote, Maha;
del Mundo, Imee M A;
Klattenhoff, Alex W;
Vasquez, Karen M

Publication type:

Article

Allovalent scavenging of activation domains in the transcription factor ANAC013 gears transcriptional regulation.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf065

By:

Delaforge, Elise;
Due, Amanda D;
Theisen, Frederik Friis;
Morffy, Nicolas;
O'Shea, Charlotte;
Blackledge, Martin;
Strader, Lucia C;
Skriver, Karen;
Kragelund, Birthe B

Publication type:

Article

A phosphorylation signal activates genome-wide transcriptional control by BfmR, the global regulator of Acinetobacter resistance and virulence.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 4, p. 1, doi. 10.1093/nar/gkaf063

By:

Raustad, Nicole;
Dai, Yunfei;
Iinishi, Akira;
Mohapatra, Arpita;
Soo, Mark W;
Hay, Everett;
Hernandez, Gabrielle M;
Geisinger, Edward

Publication type:

Article