Works matching IS 03051048 AND DT 2023 AND VI 51 AND IP 13

Results: 45

Achieving pan-microbiome biological insights via the dbBact knowledge base.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6593, doi. 10.1093/nar/gkad527

By:

Amir, Amnon;
Ozel, Eitan;
Haberman, Yael;
Shental, Noam

Publication type:

Article

Structural and biochemical characterization of Schlafen11 N-terminal domain.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 7053, doi. 10.1093/nar/gkad509

By:

Hou, Pengjiao;
Hao, Wei;
Qin, Bo;
Li, Mengyun;
Zhao, Rong;
Cui, Sheng

Publication type:

Article

Recruitment of transcription factor ETS1 to activated accessible regions promotes the transcriptional program of cilia genes.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6684, doi. 10.1093/nar/gkad506

By:

Zhang, Donghui;
Zhang, Chong;
Zhu, Yanmei;
Xie, Haixia;
Yue, Caifeng;
Li, Mingfeng;
Wei, Wenlu;
Peng, Yu;
Yin, Guibin;
Guo, Yunmiao;
Guan, Yiting

Publication type:

Article

Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB).

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 7036, doi. 10.1093/nar/gkad490

By:

Okeke, Damasus C;
Lidman, Jens;
Matečko-Burmann, Irena;
Burmann, Björn M

Publication type:

Article

ATM phosphorylates the FATC domain of DNA-PKcs at threonine 4102 to promote non-homologous end joining.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6770, doi. 10.1093/nar/gkad505

By:

Lu, Huiming;
Zhang, Qin;
Laverty, Daniel J;
Puncheon, Andrew C;
Augustine, Mathew M;
Williams, Gareth J;
Nagel, Zachary D;
Chen, Benjamin P C;
Davis, Anthony J

Publication type:

Article

Dual chemical labeling enables nucleotide-resolution mapping of DNA abasic sites and common alkylation damage in human mitochondrial DNA.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. e73, doi. 10.1093/nar/gkad502

By:

Liu, Chaoxing;
Le, Brandon H;
Xu, Wenyan;
Yang, Ching-Hsin;
Chen, Yu Hsuan;
Zhao, Linlin

Publication type:

Article

A meet-up of acetyl phosphate and c-di-GMP modulates BldD activity for development and antibiotic production.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6870, doi. 10.1093/nar/gkad494

By:

Fu, Yu;
Dong, Yu-Qi;
Shen, Jin-Long;
Yin, Bin-Cheng;
Ye, Bang-Ce;
You, Di

Publication type:

Article

Nanopore sensing reveals a preferential pathway for the co-translocational unfolding of a conjugative relaxase–DNA complex.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6857, doi. 10.1093/nar/gkad492

By:

Valenzuela-Gómez, Fernando;
Arechaga, Ignacio;
Cabezón, Elena

Publication type:

Article

CREEPY: CRISPR-mediated editing of synthetic episomes in yeast.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. e72, doi. 10.1093/nar/gkad491

By:

Zhao, Yu;
Coelho, Camila;
Lauer, Stephanie;
Majewski, Miłosz;
Laurent, Jon M;
Brosh, Ran;
Boeke, Jef D

Publication type:

Article

SIRT1 regulates DNA damage signaling through the PP4 phosphatase complex.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6754, doi. 10.1093/nar/gkad504

By:

Rasti, George;
Becker, Maximilian;
Vazquez, Berta N;
Espinosa-Alcantud, Maria;
Fernández-Duran, Irene;
Gámez-García, Andrés;
Ianni, Alessandro;
Gonzalez, Jessica;
Bosch-Presegué, Laia;
Marazuela-Duque, Anna;
Guitart-Solanes, Anna;
Segura-Bayona, Sandra;
Bech-Serra, Joan-Josep;
Scher, Michael;
Serrano, Lourdes;
Shankavaram, Uma;
Erdjument-Bromage, Hediye;
Tempst, Paul;
Reinberg, Danny;
Olivella, Mireia

Publication type:

Article

An amber-encoding helper phage for more efficient phage display of noncanonical amino acids.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6566, doi. 10.1093/nar/gkad488

By:

Hampton, Joshua Trae;
Cho, Chia-Chuan Dean;
Coleman, Demonta D;
Geng, Zhi Zachary;
Chen, Peng-Hsun Chase;
Dubey, Gopal K;
Sylvain, Lauralee D;
Xu, Shiqing;
Liu, Wenshe Ray

Publication type:

Article

Regulation of T7 gp2.5 binding dynamics by its C-terminal tail, template conformation and sequence.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6540, doi. 10.1093/nar/gkad485

By:

Xu, Longfu;
Cabanas-Danés, Jordi;
Halma, Matthew T J;
Heller, Iddo;
Stratmann, Sarah A;
van Oijen, Antoine M;
Lee, Seung-Joo;
Peterman, Erwin J G;
Wuite, Gijs J L

Publication type:

Article

Mutational and structural analyses of UdgX: insights into the active site pocket architecture and its evolution.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6554, doi. 10.1093/nar/gkad486

By:

Aroli, Shashanka;
Woo, Eui-Jeon;
Gopal, Balasubramanian;
Varshney, Umesh

Publication type:

Article

Prolonging genetic circuit stability through adaptive evolution of overlapping genes.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 7094, doi. 10.1093/nar/gkad484

By:

Chlebek, Jennifer L;
Leonard, Sean P;
Kang-Yun, Christina;
Yung, Mimi C;
Ricci, Dante P;
Jiao, Yongqin;
Park, Dan M

Publication type:

Article

Mechanistic insight into AP-endonuclease 1 cleavage of abasic sites at stalled replication fork mimics.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6738, doi. 10.1093/nar/gkad481

By:

Hoitsma, Nicole M;
Norris, Jessica;
Khoang, Thu H;
Kaushik, Vikas;
Chadda, Rahul;
Antony, Edwin;
Hedglin, Mark;
Freudenthal, Bret D

Publication type:

Article

Insights into a viral motor: the structure of the HK97 packaging termination assembly.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 7025, doi. 10.1093/nar/gkad480

By:

Hawkins, Dorothy E D P;
Bayfield, Oliver W;
Fung, Herman K H;
Grba, Daniel N;
Huet, Alexis;
Conway, James F;
Antson, Alfred A

Publication type:

Article

Polycomb protein SCML2 mediates paternal epigenetic inheritance through sperm chromatin.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6668, doi. 10.1093/nar/gkad479

By:

Sakashita, Akihiko;
Ooga, Masatoshi;
Otsuka, Kai;
Maezawa, So;
Takeuchi, Chikara;
Wakayama, Sayaka;
Wakayama, Teruhiko;
Namekawa, Satoshi H

Publication type:

Article

Sordarin bound eEF2 unlocks spontaneous forward and reverse translocation on CrPV IRES.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6999, doi. 10.1093/nar/gkad476

By:

Ou, Zheren;
Petrov, Alexey

Publication type:

Article

Active in vivo translocation of the Methanosarcina mazei Gö1 Casposon.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6927, doi. 10.1093/nar/gkad474

By:

Gehlert, Finn O;
Nickel, Lisa;
Vakirlis, Nikolaos;
Hammerschmidt, Katrin;
Vargas Gebauer, Herman I;
Kießling, Claudia;
Kupczok, Anne;
Schmitz, Ruth A

Publication type:

Article

Cas1–Cas2 physically and functionally interacts with DnaK to modulate CRISPR Adaptation.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6914, doi. 10.1093/nar/gkad473

By:

Killelea, Tom;
Dimude, Juachi U;
He, Liu;
Stewart, Alison L;
Kemm, Fiona E;
Radovčić, Marin;
Ivančić-Baće, Ivana;
Rudolph, Christian J;
Bolt, Edward L

Publication type:

Article

Single-molecule characterization of target search dynamics of DNA-binding proteins in DNA-condensed droplets.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6654, doi. 10.1093/nar/gkad471

By:

Kamagata, Kiyoto;
Kusano, Ryo;
Kanbayashi, Saori;
Banerjee, Trishit;
Takahashi, Hiroto

Publication type:

Article

Phosphorylation status of MUS81 is a modifier of Olaparib sensitivity in BRCA2-deficient cells.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6723, doi. 10.1093/nar/gkad470

By:

Blandino, Francesca;
Malacaria, Eva;
Figlioli, Carolina;
Noto, Alessandro;
Pugliese, Giusj Monia;
Franchitto, Annapaola;
Pichierri, Pietro

Publication type:

Article

NOVA1 prevents overactivation of the unfolded protein response and facilitates chromatin access during human white adipogenesis.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6981, doi. 10.1093/nar/gkad469

By:

Yang, Zhigang;
Dong, Ping;
Cao, Jiankun;
Lin, Na;
Ma, Shize;
Cao, Rui;
Cai, Lei;
Wang, Lei;
Cao, Changchang;
Xue, Yuanchao;
Pan, Jing;
Li, Xiu;
Wang, Kang;
Liu, Qiwei;
Li, Chen;
Gong, Fuxing;
Fu, Xin;
Xiao, Ran

Publication type:

Article

Multidimensional profiling reveals GATA1-modulated stage-specific chromatin states and functional associations during human erythropoiesis.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6634, doi. 10.1093/nar/gkad468

By:

Li, Dong;
Zhao, Xin-Ying;
Zhou, Shuo;
Hu, Qi;
Wu, Fan;
Lee, Hsiang-Ying

Publication type:

Article

ncOrtho: efficient and reliable identification of miRNA orthologs.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. e71, doi. 10.1093/nar/gkad467

By:

Langschied, Felix;
Leisegang, Matthias S;
Brandes, Ralf P;
Ebersberger, Ingo

Publication type:

Article

Efficient and sensitive profiling of RNA–protein interactions using TLC-CLIP.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. e70, doi. 10.1093/nar/gkad466

By:

Ernst, Christina;
Duc, Julien;
Trono, Didier

Publication type:

Article

On the accuracy of the epigenetic copy machine: comprehensive specificity analysis of the DNMT1 DNA methyltransferase.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6622, doi. 10.1093/nar/gkad465

By:

Adam, Sabrina;
Klingel, Viviane;
Radde, Nicole E;
Bashtrykov, Pavel;
Jeltsch, Albert

Publication type:

Article

eEF2 diphthamide modification restrains spurious frameshifting to maintain translational fidelity.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6899, doi. 10.1093/nar/gkad461

By:

Shin, Byung-Sik;
Ivanov, Ivaylo P;
Kim, Joo-Ran;
Cao, Chune;
Kinzy, Terri G;
Dever, Thomas E

Publication type:

Article

A method to generate capture baits for targeted sequencing.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. e69, doi. 10.1093/nar/gkad460

By:

Sundararaman, Balaji;
Vershinina, Alisa O;
Hershauer, Samantha;
Kapp, Joshua D;
Dunn, Shelby;
Shapiro, Beth;
Green, Richard E

Publication type:

Article

A rapid protocol for ribosome profiling of low input samples.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. e68, doi. 10.1093/nar/gkad459

By:

Meindl, Andreas;
Romberger, Markus;
Lehmann, Gerhard;
Eichner, Norbert;
Kleemann, Leon;
Wu, Jie;
Danner, Johannes;
Boesl, Maria;
Mesitov, Mikhail;
Meister, Gunter;
König, Julian;
Leidel, Sebastian Andreas;
Medenbach, Jan

Publication type:

Article

DUF2285 is a novel helix-turn-helix domain variant that orchestrates both activation and antiactivation of conjugative element transfer in proteobacteria.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6841, doi. 10.1093/nar/gkad457

By:

Jowsey, William J;
Morris, Calum R P;
Hall, Drew A;
Sullivan, John T;
Fagerlund, Robert D;
Eto, Karina Y;
Solomon, Paul D;
Mackay, Joel P;
Bond, Charles S;
Ramsay, Joshua P;
Ronson, Clive W

Publication type:

Article

Efficient gene activation in plants by the MoonTag programmable transcriptional activator.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 7083, doi. 10.1093/nar/gkad458

By:

Casas-Mollano, J Armando;
Zinselmeier, Matthew H;
Sychla, Adam;
Smanski, Michael J

Publication type:

Article

Reducing the inherent auto-inhibitory interaction within the pegRNA enhances prime editing efficiency.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6966, doi. 10.1093/nar/gkad456

By:

Ponnienselvan, Karthikeyan;
Liu, Pengpeng;
Nyalile, Thomas;
Oikemus, Sarah;
Maitland, Stacy A;
Lawson, Nathan D;
Luban, Jeremy;
Wolfe, Scot A

Publication type:

Article

Trypanosome RNA helicase KREH2 differentially controls non-canonical editing and putative repressive structure via a novel proposed 'bifunctional' gRNA in mRNA A6.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6944, doi. 10.1093/nar/gkad453

By:

Meehan, Joshua;
McDermott, Suzanne M;
Ivens, Alasdair;
Goodall, Zachary;
Chen, Zihao;
Yu, Zihao;
Woo, Jia;
Rodshagen, Tyler;
McCleskey, Laura;
Sechrist, Rebecca;
Stuart, Kenneth;
Zeng, Lanying;
Rouskin, Silvi;
Savill, Nicholas J;
Schnaufer, Achim;
Zhang, Xiuren;
Cruz-Reyes, Jorge

Publication type:

Article

Restriction-modification systems have shaped the evolution and distribution of plasmids across bacteria.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6806, doi. 10.1093/nar/gkad452

By:

Shaw, Liam P;
Rocha, Eduardo P C;
MacLean, R Craig

Publication type:

Article

Design of synthetic promoters for cyanobacteria with generative deep-learning model.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 7071, doi. 10.1093/nar/gkad451

By:

Seo, Euijin;
Choi, Yun-Nam;
Shin, Ye Rim;
Kim, Donghyuk;
Lee, Jeong Wook

Publication type:

Article

Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6578, doi. 10.1093/nar/gkad450

By:

Yang, Yongjian;
Li, Guanxun;
Zhong, Yan;
Xu, Qian;
Chen, Bo-Jia;
Lin, Yu-Te;
Chapkin, Robert S;
Cai, James J

Publication type:

Article

IFI16 phase separation via multi-phosphorylation drives innate immune signaling.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6819, doi. 10.1093/nar/gkad449

By:

Liu, Dawei;
Lum, Krystal K;
Treen, Nicholas;
Núñez, Corazón T;
Yang, Jinhang;
Howard, Timothy R;
Levine, Michael;
Cristea, Ileana M

Publication type:

Article

The THO complex counteracts TERRA R-loop-mediated telomere fragility in telomerase+ cells and telomeric recombination in ALT+ cells.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6702, doi. 10.1093/nar/gkad448

By:

Fernandes, Rita Valador;
Lingner, Joachim

Publication type:

Article

Protein oxidation increases SAMHD1 binding ssDNA via its regulatory site.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 7014, doi. 10.1093/nar/gkad447

By:

Simermeyer, Theresa L;
Batalis, Stephanie;
Rogers, LeAnn C;
Zalesak, Owen J;
Hollis, Thomas

Publication type:

Article

High fidelity DNA strand-separation is the major specificity determinant in DNA methyltransferase CcrM's catalytic mechanism.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6883, doi. 10.1093/nar/gkad443

By:

Konttinen, Olivia;
Carmody, Jason;
Kurnik, Martin;
Johnson, Kenneth A;
Reich, Norbert

Publication type:

Article

Enhanced nonenzymatic RNA copying with in-situ activation of short oligonucleotides.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6528, doi. 10.1093/nar/gkad439

By:

Ding, Dian;
Zhang, Stephanie J;
Szostak, Jack W

Publication type:

Article

Stochastic scanning events on the GCN4 mRNA 5' untranslated region generate cell-to-cell heterogeneity in the yeast nutritional stress response.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6609, doi. 10.1093/nar/gkad433

By:

Meng, Xiang;
Reed, Alan;
Lai, Sandie;
Szavits-Nossan, Juraj;
McCarthy, John E G

Publication type:

Article

Multiomic analysis of cohesin reveals that ZBTB transcription factors contribute to chromatin interactions.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6784, doi. 10.1093/nar/gkad401

By:

Wang, Rui;
Xu, Qiqin;
Wang, Chenlu;
Tian, Kai;
Wang, Hui;
Ji, Xiong

Publication type:

Article

Induction of the alternative lengthening of telomeres pathway by trapping of proteins on DNA.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 13, p. 6509, doi. 10.1093/nar/gkad150

By:

Rose, Anna M;
Goncalves, Tomas;
Cunniffe, Siobhan;
Geiller, Helene E B;
Kent, Thomas;
Shepherd, Sam;
Ratnaweera, Malitha;
O'Sullivan, Roderick J;
Gibbons, Richard J;
Clynes, David

Publication type:

Article