Works in Nucleic Acids Research, 2025, Vol 53, Issue 8

Results: 38

Human DNA replication initiation sites are specified epigenetically by oxidation of 5-methyl-deoxycytidine Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf362

By:

Krude, Torsten;
Bi, Jiaming;
Doran, Rachel;
Jones, Rebecca A;
Smith, James C

Publication type:

Article

Correction to 'Nitric oxide controls nuclear export of APE1/Ref-1 through S-nitrosation of Cysteines 93 and 310' Open Access.

Published in:: 2025
Publication type:: Correction Notice

Correction to '8-Oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutSα' Open Access.

Published in:: 2025
Publication type:: Correction Notice

Mapping effective microRNA pairing beyond the seed using abasic modifications Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf364

By:

Kosek, David M;
Petzold, Katja;
Andersson, Emma R

Publication type:

Article

Histone tetrasome dynamics affects chromatin transcription Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf356

By:

Shi, Xiangyan;
Fedulova, Anastasiia S;
Kotova, Elena Y;
Maluchenko, Natalya V;
Armeev, Grigoriy A;
Chen, Qinming;
Prasanna, Chinmayi;
Sivkina, Anastasia L;
Feofanov, Alexey V;
Kirpichnikov, Mikhail P;
Nordensköld, Lars;
Shaytan, Alexey K;
Studitsky, Vasily M

Publication type:

Article

CARM1/PRMT4 facilitates XPF–ERCC1 heterodimer assembly and maintains nucleotide excision repair activity Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf355

By:

Niida, Hiroyuki;
Ito, Masahiko;
Iijima, Kenta;
Motegi, Akira;
Ogihara, Rin;
Akiyama, Hironobu;
Uchida, Chiharu;
Sakai, Satoshi;
Ohhata, Tatsuya;
Hatano, Atsushi;
Hirose, Michiko;
Ogura, Atsuo;
Matsumoto, Masaki;
McDonald, Neil Q;
Kitagawa, Masatoshi

Publication type:

Article

A CRISPR-SpCas9M-reporting system for efficient and rapid genome editing in Caulobacter crescentusOpen Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf353

By:

Sun, Jingxian;
Yu, Xin;
Tang, Guiyue;
Chen, Mengqing;
Zheng, Yixin;
Hu, Yucan;
Li, Qingmei;
Li, Xiaoyang;
Li, Ningning;
Li, Zhongyue;
Li, Yingying;
Lu, Ning;
Tan, Wei;
Yang, Yujiao;
Lyu, Xiaoye;
Zhao, Guohong;
Wang, Hailong;
Dai, Lei;
Zhao, Guo-Ping;
Ai, Lianzhong

Publication type:

Article

Replicative DNA polymerase epsilon and delta holoenzymes show wide-ranging inhibition at G-quadruplexes in the human genome Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf352

By:

Hile, Suzanne E;
Weissensteiner, Matthias H;
Pytko, Kara G;
Dahl, Joseph;
Kejnovsky, Eduard;
Kejnovská, Iva;
Hedglin, Mark;
Georgakopoulos-Soares, Ilias;
Makova, Kateryna D;
Eckert, Kristin A

Publication type:

Article

Mechanistic insights into the activity of SARS-CoV-2 RNA polymerase inhibitors using single-molecule FRET Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf351

By:

Groves, Danielle;
Cunnison, Rory;
McMahon, Andrew;
Fan, Haitian;
Sharps, Jane;
Deng, Adrian;
Keown, Jeremy R;
Fodor, Ervin;
Robb, Nicole C

Publication type:

Article

METTL3-dependent m6A RNA methylation regulates transposable elements and represses human naïve pluripotency through transposable element-derived enhancers Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf349

By:

Zhang, Weiyu;
Fu, Haifeng;
Huang, Yunying;
Zeng, Ming;
Ouyang, Xiangyu;
Wang, Xiao;
Ruan, Degong;
Ma, Liyang;
Hu, Xinning;
Guo, Jilong;
Galardi, Justin W;
Dougan, Gordon;
Yeung, William S B;
Li, Lei;
Liu, Jianqiao;
Feschotte, Cedric;
Liu, Pentao

Publication type:

Article

FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf348

By:

Gerhardt, Kenji;
Ruiz-Perez, Carlos A;
Rodriguez-R, Luis M;
Jain, Chirag;
Tiedje, James M;
Cole, James R;
Konstantinidis, Konstantinos T

Publication type:

Article

Bimodal specificity of TF–DNA recognition in embryonic stem cells Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf333

By:

Povolotskii, Michael;
Yehezkehely, Maor;
Ram, Oren;
Lukatsky, David B

Publication type:

Article

The N=1 Collaborative: advancing customized nucleic acid therapies through collaboration and data sharing Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf346

By:

Belgrad, Jillian;
McConnell, Erin;
Leonard, Stef;
Nolen, Nicole;
Lauffer, Marlen C;
Watts, Jonathan K;
Yu, Timothy;
Yan, Winston X;
Aartsma-Rus, Annemieke

Publication type:

Article

Dynamic activation of rAAV transgene expression by a small molecule that recruits endogenous transcriptional machinery Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf345

By:

Wasserman, Sara R;
Muron, Savannah;
Lee, Hae Rim;
Routh, Madison L;
Hepperla, Austin J;
Scoville, Deena M;
Huber, Avery;
Umana, Jessica D;
Pereira, Nicole E;
Foley, Caroline A;
James, Lindsey I;
Hathaway, Nathaniel A

Publication type:

Article

Donor insertion into CX3CR1 allows epigenetic modulation of a constitutive promoter on hematopoietic stem cells and its activation upon myeloid differentiation Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf344

By:

Ramos-Hernández, Iris;
Fuster-García, Carla;
Aguilar-González, Araceli;
Lozano-Vinagre, María L;
Guenechea-Amurrio, Guillermo;
Sanchez-Luque, Francisco J;
Gonçalves, Manuel A F V;
Cathomen, Toni;
Muñoz, Pilar;
Molina-Estévez, Francisco J;
Martín, Francisco

Publication type:

Article

Molecular basis of Streptomyces ECF σShbA factors transcribing principal σHrdB genes Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf339

By:

Liu, Guiyang;
Yang, Xu;
Yan, Wenjin;
Wang, Yiqun;
Yu, Feng;
Zheng, Jianting

Publication type:

Article

PRMT5 promotes full-length HTT expression by repressing multiple proximal intronic polyadenylation sites Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf347

By:

Yadav, Manisha;
AlQazzaz, Mona A;
Ciamponi, Felipe E;
Ho, Jolene C;
Maron, Maxim I;
Sababi, Aiden M;
MacLeod, Graham;
Ahmadi, Moloud;
Bullivant, Garrett;
Tano, Vincent;
Langley, Sarah R;
Sánchez-Osuna, María;
Sachamitr, Patty;
Kushida, Michelle;
Bardile, Costanza Ferrari;
Pouladi, Mahmoud A;
Kurtz, Rebecca;
Richards, Laura;
Pugh, Trevor;
Tyers, Mike

Publication type:

Article

Different propensities for gate opening in gyrases and topoisomerase IV Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf330

By:

Willing, Florian;
Mhaindarkar, Vaibhav P;
Hirsch, Jana;
Lanz, Martin A;
Mitton-Fry, Mark J;
Gubaev, Airat;
Klostermeier, Dagmar

Publication type:

Article

invertiaDB: a database of inverted repeats across organismal genomes Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf329

By:

Provatas, Kimonas;
Chantzi, Nikol;
Amptazi, Nafsika;
Patsakis, Michail;
Nayak, Akshatha;
Mouratidis, Ioannis;
Zaravinos, Apostolos;
Pavlopoulos, Georgios A;
Georgakopoulos-Soares, Ilias

Publication type:

Article

Unexpected enzymatic function of an ancient nucleic acid-binding fold Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf328

By:

Watkins, Rylan R;
Bockelman, Stella;
Vradi, Anna;
Grabarkewitz, Kaylee;
Pyun, Alexa;
Stark, Josephine;
Wysocki, Vicki H;
Alfonzo, Juan D;
Musier-Forsyth, Karin

Publication type:

Article

Monitoring monomer-specific acyl–tRNA levels in cells with PARTI Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf327

By:

Pressimone, Meghan A;
Schissel, Carly K;
Goss, Isabella H;
Swenson, Cameron V;
Schepartz, Alanna

Publication type:

Article

The structure of the Vibrio natriegens 70S ribosome in complex with the proline-rich antimicrobial peptide Bac5(1–17) Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf324

By:

Raulf, Karoline;
Koller, Timm O;
Beckert, Bertrand;
Lepak, Alexander;
Morici, Martino;
Mardirossian, Mario;
Scocchi, Marco;
Bange, Gert;
Wilson, Daniel N

Publication type:

Article

Archaeal replicative primase mediates DNA double-strand break repair Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf322

By:

Xiong, Daijiang;
Li, Zhimeng;
Qi, Wen;
Wang, Shaoying;
Huang, Junkai;
Zhang, Ningning;
Zhang, Zhenfeng;
Huang, Li

Publication type:

Article

A structural element within the 5′UTR of β-catenin mRNA modulates its translation under hypoxia Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf321

By:

D'Agostino, Mattia;
Rol-Moreno, Javier;
Bec, Guillaume;
Kuhn, Lauriane;
Ennifar, Eric;
Simonetti, Angelita

Publication type:

Article

DYRK1B phosphorylates FOXO1 to promote hepatic gluconeogenesis Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf319

By:

Li, Shanshan;
Huang, Kai;
Xu, Chu;
Zhang, Hong;
Wang, Xiao;
Zhang, Rong;
Lu, Yan;
Mohan, Man;
Hu, Cheng

Publication type:

Article

Mechanism of Cas9 inhibition by AcrIIA11 Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf318

By:

Dillard, Kaylee E;
Zhang, Hongshan;
Dubbs, Lianne Z;
Chou, Chia-Wei;
Terrace, Cynthia;
Javanmardi, Kamyab;
Kim, Wantae;
Forsberg, Kevin J;
Finkelstein, Ilya J

Publication type:

Article

A powerful and highly efficient PAI-mediated transgenesis approach in DrosophilaOpen Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf317

By:

Shi, Wangfei;
Zhang, Xuedi;
Sun, Angyang;
Zheng, Jie;
Zhuang, Kailong;
Chen, Ziheng;
Peng, Ju;
Fu, Pengchong;
Gao, Guanjun

Publication type:

Article

The SAS chromatin-remodeling complex mediates inflorescence-specific chromatin accessibility for transcription factor binding Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf316

By:

Guo, Jing;
Liu, Zhen-Zhen;
Su, Xiao-Min;
Su, Yin-Na;
He, Xin-Jian

Publication type:

Article

Advancing RNA phage biology through meta-omics Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf314

By:

Hör, Jens

Publication type:

Article

DirectHRD enables sensitive scar-based classification of homologous recombination deficiency Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf313

By:

Liu, Ruolin;
Roberts, Eugenia;
Parsons, Heather A;
Stover, Elizabeth H;
Choudhury, Atish D;
Rhoades, Justin;
Blewett, Timothy;
Yang, David D;
Liu, Joyce F;
Mayer, Erica L;
Adalsteinsson, Viktor A

Publication type:

Article

HU promotes higher order chromosome organization and influences DNA replication rates in Streptococcus pneumoniaeOpen Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf312

By:

Mazzuoli, Maria-Vittoria;
van Raaphorst, Renske;
Martin, Louise S;
Bock, Florian P;
Thierry, Agnès;
Marbouty, Martial;
Waclawiková, Barbora;
Stinenbosch, Jasper;
Koszul, Romain;
Veening, Jan-Willem

Publication type:

Article

Exploring the effect of activator topology on CRISPR–Cas12a trans-cleavage activity Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf311

By:

Zhu, Zixuan;
Li, Xiaolong;
Ding, Lin;
Wu, Tongbo

Publication type:

Article

Correction to 'PfGCN5 is essential for Plasmodium falciparum survival and transmission and regulates Pf H2B.Z acetylation and chromatin structure' Open Access.

Published in:: 2025
Publication type:: Correction Notice

Deciphering the human TopIIIα activity modulated by Rmi1 using magnetic tweezers Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf308

By:

Yun, Long;
Garnier, Florence;
Strick, Terence R;
Nadal, Marc

Publication type:

Article

A non-tethering role for the Drosophila Pol θ linker domain in promoting damage resolution Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf304

By:

Blanch, Justin R;
Woodward, Nicholas;
Krishnamurthy, Manan;
McVey, Mitch

Publication type:

Article

Translational activity of 80S monosomes varies dramatically across different tissues Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf292

By:

Blandy, Albert;
Hopes, Tayah;
Vasconcelos, Elton J R;
Turner, Amy;
Fatkhullin, Bulat;
Agapiou, Michaela;
Fontana, Juan;
Aspden, Julie L

Publication type:

Article

Natronobacterium gregoryi Argonaute inhibits class 1 integron integrase-mediated excision and integration Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf248

By:

Zeng, Yue;
Tan, Xin;
Xiao, Peng;
Gao, Peiying;
Wang, Libo;
Zhang, Anding

Publication type:

Article

RNA G-quadruplex removal promotes a translational switch after meiosis resumption Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 8, p. 1, doi. 10.1093/nar/gkaf067

By:

Lu, Qiong-Wen;
Liu, Shao-Yuan;
Liao, Xiu-Quan;
Chen, Jing;
Jiang, Zhi-Yan;
Wu, Yu-Ke;
Fan, Heng-Yu;
Lu, Yu-Jing;
Sha, Qian-Qian

Publication type:

Article

Works in Nucleic Acids Research, 2025, Vol 53, Issue 8

Human DNA replication initiation sites are specified epigenetically by oxidation of 5-methyl-deoxycytidine Open Access.

Correction to 'Nitric oxide controls nuclear export of APE1/Ref-1 through S-nitrosation of Cysteines 93 and 310' Open Access.

Correction to '8-Oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutSα' Open Access.

Mapping effective microRNA pairing beyond the seed using abasic modifications Open Access.

Histone tetrasome dynamics affects chromatin transcription Open Access.

CARM1/PRMT4 facilitates XPF–ERCC1 heterodimer assembly and maintains nucleotide excision repair activity Open Access.

A CRISPR-SpCas9M-reporting system for efficient and rapid genome editing in Caulobacter crescentusOpen Access.

Replicative DNA polymerase epsilon and delta holoenzymes show wide-ranging inhibition at G-quadruplexes in the human genome Open Access.

Mechanistic insights into the activity of SARS-CoV-2 RNA polymerase inhibitors using single-molecule FRET Open Access.

METTL3-dependent m<sup>6</sup>A RNA methylation regulates transposable elements and represses human naïve pluripotency through transposable element-derived enhancers Open Access.

FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins Open Access.

Bimodal specificity of TF–DNA recognition in embryonic stem cells Open Access.

The N=1 Collaborative: advancing customized nucleic acid therapies through collaboration and data sharing Open Access.

Dynamic activation of rAAV transgene expression by a small molecule that recruits endogenous transcriptional machinery Open Access.

Donor insertion into CX3CR1 allows epigenetic modulation of a constitutive promoter on hematopoietic stem cells and its activation upon myeloid differentiation Open Access.

Molecular basis of Streptomyces ECF σ<sup>ShbA</sup> factors transcribing principal σ<sup>HrdB</sup> genes Open Access.

PRMT5 promotes full-length HTT expression by repressing multiple proximal intronic polyadenylation sites Open Access.

Different propensities for gate opening in gyrases and topoisomerase IV Open Access.

invertiaDB: a database of inverted repeats across organismal genomes Open Access.

Unexpected enzymatic function of an ancient nucleic acid-binding fold Open Access.

Monitoring monomer-specific acyl–tRNA levels in cells with PARTI Open Access.

The structure of the Vibrio natriegens 70S ribosome in complex with the proline-rich antimicrobial peptide Bac5(1–17) Open Access.

Archaeal replicative primase mediates DNA double-strand break repair Open Access.

A structural element within the 5′UTR of β-catenin mRNA modulates its translation under hypoxia Open Access.

DYRK1B phosphorylates FOXO1 to promote hepatic gluconeogenesis Open Access.

Mechanism of Cas9 inhibition by AcrIIA11 Open Access.

A powerful and highly efficient PAI-mediated transgenesis approach in DrosophilaOpen Access.

The SAS chromatin-remodeling complex mediates inflorescence-specific chromatin accessibility for transcription factor binding Open Access.

Advancing RNA phage biology through meta-omics Open Access.

DirectHRD enables sensitive scar-based classification of homologous recombination deficiency Open Access.

HU promotes higher order chromosome organization and influences DNA replication rates in Streptococcus pneumoniaeOpen Access.

Exploring the effect of activator topology on CRISPR–Cas12a trans-cleavage activity Open Access.

Correction to 'PfGCN5 is essential for Plasmodium falciparum survival and transmission and regulates Pf H2B.Z acetylation and chromatin structure' Open Access.

Deciphering the human TopIIIα activity modulated by Rmi1 using magnetic tweezers Open Access.

A non-tethering role for the Drosophila Pol θ linker domain in promoting damage resolution Open Access.

Translational activity of 80S monosomes varies dramatically across different tissues Open Access.

Natronobacterium gregoryi Argonaute inhibits class 1 integron integrase-mediated excision and integration Open Access.

RNA G-quadruplex removal promotes a translational switch after meiosis resumption Open Access.