Works matching IS 03051048 AND DT 2024 AND VI 52 AND IP 3

Results: 42

Correction to 'Using energy to go downhill—a genoprotective role for ATPase activity in DNA topoisomerase II'.

Published in:: 2024
Publication type:: Correction Notice

Minimization of the E. coli ribosome, aided and optimized by community science.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1027, doi. 10.1093/nar/gkad1254

By:

Tangpradabkul, Tiyaporn;
Palo, Michael;
Townley, Jill;
Hsu, Kenneth B;
participants, Eterna;
Smaga, Sarah;
Das, Rhiju;
Schepartz, Alanna

Publication type:

Article

The roles of DNA methylation on pH dependent i-motif (iM) formation in rice.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1243, doi. 10.1093/nar/gkad1245

By:

Feng, Yilong;
Ma, Xing;
Yang, Ying;
Tao, Shentong;
Ahmed, Asgar;
Gong, Zhiyun;
Cheng, Xuejiao;
Zhang, Wenli

Publication type:

Article

Correction to 'Effective extraction of polyribosomes exposes gene expression strategies in primary astrocytes'.

Published in:: 2024
Publication type:: Correction Notice

Correction to 'Srsf1 and Elavl1 act antagonistically on neuronal fate choice in the developing neocortex by controlling TrkC receptor isoform expression'.

Published in:: 2024
Publication type:: Correction Notice

Enhancing circuit stability under growth feedback with supplementary repressive regulation.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1512, doi. 10.1093/nar/gkad1233

By:

Stone, Austin;
Rijal, Sadikshya;
Zhang, Rong;
Tian, Xiao-Jun

Publication type:

Article

Structural basis for transcription activation by the nitrate-responsive regulator NarL.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1471, doi. 10.1093/nar/gkad1231

By:

Kompaniiets, Dmytro;
He, Lina;
Wang, Dong;
Zhou, Wei;
Yang, Yang;
Hu, Yangbo;
Liu, Bin

Publication type:

Article

Rapid human genomic DNA cloning into mouse artificial chromosome via direct chromosome transfer from human iPSC and CRISPR/Cas9-mediated translocation.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1498, doi. 10.1093/nar/gkad1218

By:

Miyamoto, Hitomaru;
Kobayashi, Hiroaki;
Kishima, Nanami;
Yamazaki, Kyotaro;
Hamamichi, Shusei;
Uno, Narumi;
Abe, Satoshi;
Hiramuki, Yosuke;
Kazuki, Kanako;
Tomizuka, Kazuma;
Kazuki, Yasuhiro

Publication type:

Article

Scaffold RNA engineering in type V CRISPR-Cas systems: a potent way to enhance gene expression in the yeast Saccharomyces cerevisiae.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1483, doi. 10.1093/nar/gkad1216

By:

Yu, Lifang;
Marchisio, Mario Andrea

Publication type:

Article

Recent reactivation of a pathogenicity-associated transposable element is associated with major chromosomal rearrangements in a fungal wheat pathogen.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1226, doi. 10.1093/nar/gkad1214

By:

Badet, Thomas;
Tralamazza, Sabina Moser;
Feurtey, Alice;
Croll, Daniel

Publication type:

Article

Reappraisal of the DNA phosphorothioate modification machinery: uncovering neglected functional modalities and identification of new counter-invader defense systems.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1005, doi. 10.1093/nar/gkad1213

By:

Rakesh, Siuli;
Aravind, L;
Krishnan, Arunkumar

Publication type:

Article

Harmonin homology domain-mediated interaction of RTEL1 helicase with RPA and DNA provides insights into its recruitment to DNA repair sites.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1450, doi. 10.1093/nar/gkad1208

By:

Kumar, Niranjan;
Taneja, Arushi;
Ghosh, Meenakshi;
Rothweiler, Ulli;
Sundaresan, Nagalingam Ravi;
Singh, Mahavir

Publication type:

Article

A phage-encoded RNA-binding protein inhibits the antiviral activity of a toxin–antitoxin system.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1298, doi. 10.1093/nar/gkad1207

By:

Guegler, Chantal K;
Teodoro, Gabriella I C;
Srikant, Sriram;
Chetlapalli, Keerthana;
Doering, Christopher R;
Ghose, Dia A;
Laub, Michael T

Publication type:

Article

Light-strand bias and enriched zones of embedded ribonucleotides are associated with DNA replication and transcription in the human-mitochondrial genome.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1207, doi. 10.1093/nar/gkad1204

By:

Xu, Penghao;
Yang, Taehwan;
Kundnani, Deepali L;
Sun, Mo;
Marsili, Stefania;
Gombolay, Alli L;
Jeon, Youngkyu;
Newnam, Gary;
Balachander, Sathya;
Bazzani, Veronica;
Baccarani, Umberto;
Park, Vivian S;
Tao, Sijia;
Lori, Adriana;
Schinazi, Raymond F;
Kim, Baek;
Pursell, Zachary F;
Tell, Gianluca;
Vascotto, Carlo;
Storici, Francesca

Publication type:

Article

Structure of the WYL-domain containing transcription activator, DriD, in complex with ssDNA effector and DNA target site.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1435, doi. 10.1093/nar/gkad1198

By:

Schumacher, Maria A;
Cannistraci, Emily;
Salinas, Raul;
Lloyd, Devin;
Messner, Ella;
Gozzi, Kevin

Publication type:

Article

Pathological mutations promote proteolysis of mitochondrial tRNA-specific 2-thiouridylase 1 (MTU1) via mitochondrial caseinolytic peptidase (CLPP).

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1341, doi. 10.1093/nar/gkad1197

By:

Ahmad, Raja Norazireen Raja;
Zhang, Long-Teng;
Morita, Rikuri;
Tani, Haruna;
Wu, Yong;
Chujo, Takeshi;
Ogawa, Akiko;
Harada, Ryuhei;
Shigeta, Yasuteru;
Tomizawa, Kazuhito;
Wei, Fan-Yan

Publication type:

Article

An exonuclease-resistant chain-terminating nucleotide analogue targeting the SARS-CoV-2 replicase complex.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1325, doi. 10.1093/nar/gkad1194

By:

Shannon, Ashleigh;
Chazot, Aurélie;
Feracci, Mikael;
Falcou, Camille;
Fattorini, Véronique;
Selisko, Barbara;
Good, Steven;
Moussa, Adel;
Sommadossi, Jean-Pierre;
Ferron, François;
Alvarez, Karine;
Canard, Bruno

Publication type:

Article

Spatial regulation of DNA damage tolerance protein Rad5 interconnects genome stability maintenance and proteostasis networks.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1156, doi. 10.1093/nar/gkad1176

By:

Lehmann, Carl P;
González-Fernández, Paula;
Tercero, José Antonio

Publication type:

Article

Gene set correlation enrichment analysis for interpreting and annotating gene expression profiles.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. e17, doi. 10.1093/nar/gkad1187

By:

Chang, Lan-Yun;
Lee, Meng-Zhan;
Wu, Yujia;
Lee, Wen-Kai;
Ma, Chia-Liang;
Chang, Jun-Mao;
Chen, Ciao-Wen;
Huang, Tzu-Chun;
Lee, Chia-Hwa;
Lee, Jih-Chin;
Tseng, Yu-Yao;
Lin, Chun-Yu

Publication type:

Article

cGAS-STING signalling regulates microglial chemotaxis in genome instability.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1188, doi. 10.1093/nar/gkad1184

By:

Talbot, Emily J;
Joshi, Lisha;
Thornton, Peter;
Dezfouli, Mahya;
Tsafou, Kalliopi;
Perkinton, Michael;
Khoronenkova, Svetlana V

Publication type:

Article

Global analysis of binding sites of U2AF1 and ZRSR2 reveals RNA elements required for mutually exclusive splicing by the U2- and U12-type spliceosome.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1420, doi. 10.1093/nar/gkad1180

By:

Kwon, Young-Soo;
Jin, Sang Woo;
Song, Hoseok

Publication type:

Article

The protein phosphatase EYA4 promotes homologous recombination (HR) through dephosphorylation of tyrosine 315 on RAD51.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1173, doi. 10.1093/nar/gkad1177

By:

de la Peña Avalos, Bárbara;
Paquet, Nicolas;
Tropée, Romain;
Coulombe, Yan;
Palacios, Hannah;
Leung, Justin W;
Masson, Jean-Yves;
Duijf, Pascal H G;
Dray, Eloïse

Publication type:

Article

Replication elongates short DNA, reduces sequence bias and develops trimer structure.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1290, doi. 10.1093/nar/gkad1190

By:

Calaça Serrão, Adriana;
Dänekamp, Felix T;
Meggyesi, Zsófia;
Braun, Dieter

Publication type:

Article

HetFCM: functional co-module discovery by heterogeneous network co-clustering.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. e16, doi. 10.1093/nar/gkad1174

By:

Tan, Haojiang;
Guo, Maozu;
Chen, Jian;
Wang, Jun;
Yu, Guoxian

Publication type:

Article

The previously uncharacterized RnpM (YlxR) protein modulates the activity of ribonuclease P in Bacillus subtilis in vitro.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1404, doi. 10.1093/nar/gkad1171

By:

Wicke, Dennis;
Neumann, Piotr;
Gößringer, Markus;
Chernev, Aleksandar;
Davydov, Swetlana;
Poehlein, Anja;
Daniel, Rolf;
Urlaub, Henning;
Hartmann, Roland K;
Ficner, Ralf;
Stülke, Jörg

Publication type:

Article

Pasa: leveraging population pangenome graph to scaffold prokaryote genome assemblies.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. e15, doi. 10.1093/nar/gkad1170

By:

Do, Van Hoan;
Nguyen, Son Hoang;
Le, Duc Quang;
Nguyen, Tam Thi;
Nguyen, Canh Hao;
Ho, Tho Huu;
Vo, Nam S;
Nguyen, Trang;
Nguyen, Hoang Anh;
Cao, Minh Duc

Publication type:

Article

Differentiable partition function calculation for RNA.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. e14, doi. 10.1093/nar/gkad1168

By:

Matthies, Marco C;
Krueger, Ryan;
Torda, Andrew E;
Ward, Max

Publication type:

Article

Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. e13, doi. 10.1093/nar/gkad1167

By:

Baldoni, Pedro L;
Chen, Yunshun;
Hediyeh-zadeh, Soroor;
Liao, Yang;
Dong, Xueyi;
Ritchie, Matthew E;
Shi, Wei;
Smyth, Gordon K

Publication type:

Article

Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1107, doi. 10.1093/nar/gkad1164

By:

Loza, Martin;
Vandenbon, Alexis;
Nakai, Kenta

Publication type:

Article

Using transition density models to interpret experimental optical spectra of exciton-coupled cyanine (iCy3)<sub>2</sub> dimer probes of local DNA conformations at or near functional protein binding sites.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1272, doi. 10.1093/nar/gkad1163

By:

Heussman, Dylan;
Enkhbaatar, Lulu;
Sorour, Mohammed I;
Kistler, Kurt A;
von Hippel, Peter H;
Matsika, Spiridoula;
Marcus, Andrew H

Publication type:

Article

Exonic splicing code and coordination of divalent metals in proteins.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1090, doi. 10.1093/nar/gkad1161

By:

Bakhtiar, Dara;
Vondraskova, Katarina;
Pengelly, Reuben J;
Chivers, Martin;
Kralovicova, Jana;
Vorechovsky, Igor

Publication type:

Article

A tailed mirtron promotes longevity in Drosophila.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1080, doi. 10.1093/nar/gkad1158

By:

Khanal, Sweta;
de Cruz, Matthew;
Strickland, Britton;
Mansfield, Kody;
Lai, Eric C;
Flynt, Alex

Publication type:

Article

Using energy to go downhill—a genoprotective role for ATPase activity in DNA topoisomerase II.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1313, doi. 10.1093/nar/gkad1157

By:

Bandak, Afif F;
Blower, Tim R;
Nitiss, Karin C;
Shah, Viraj;
Nitiss, John L;
Berger, James M

Publication type:

Article

Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. e12, doi. 10.1093/nar/gkad1153

By:

Flores, Samuel Coulbourn;
Malý, Michal;
Hrebík, Dominik;
Plevka, Pavel;
Černý, Jiří

Publication type:

Article

Functional analysis of the AUG initiator codon context reveals novel conserved sequences that disfavor mRNA translation in eukaryotes.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1064, doi. 10.1093/nar/gkad1152

By:

Hernández, Greco;
García, Alejandra;
Weingarten-Gabbay, Shira;
Mishra, Rishi Kumar;
Hussain, Tanweer;
Amiri, Mehdi;
Moreno-Hagelsieb, Gabriel;
Montiel-Dávalos, Angélica;
Lasko, Paul;
Sonenberg, Nahum

Publication type:

Article

Alternative cleavage and polyadenylation of the Ccnb1 mRNA defines accumulation of cyclin protein during the meiotic cell cycle.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1258, doi. 10.1093/nar/gkad1151

By:

Wang, Xiaotian;
Leung, Fang-Shiuan;
Bush, Jeffrey O;
Conti, Marco

Publication type:

Article

Post-transcriptional regulation shapes the transcriptome of quiescent budding yeast.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1043, doi. 10.1093/nar/gkad1147

By:

Greenlaw, Alison C;
Alavattam, Kris G;
Tsukiyama, Toshio

Publication type:

Article

DAXX promotes centromeric stability independently of ATRX by preventing the accumulation of R-loop-induced DNA double-stranded breaks.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1136, doi. 10.1093/nar/gkad1141

By:

Pinto, Lia M;
Pailas, Alexandros;
Bondarchenko, Max;
Sharma, Abhishek Bharadwaj;
Neumann, Katrin;
Rizzo, Anthony J;
Jeanty, Céline;
Nicot, Nathalie;
Racca, Carine;
Graham, Mindy K;
Naughton, Catherine;
Liu, Yaqun;
Chen, Chun-Long;
Meakin, Paul J;
Gilbert, Nick;
Britton, Sébastien;
Meeker, Alan K;
Heaphy, Christopher M;
Larminat, Florence;
Van Dyck, Eric

Publication type:

Article

Contribution of tRNA sequence and modifications to the decoding preferences of E. coli and M. mycoides tRNA<sup>Gly</sup>UCC for synonymous glycine codons.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1374, doi. 10.1093/nar/gkad1136

By:

Kompatscher, Maria;
Bartosik, Karolina;
Erharter, Kevin;
Plangger, Raphael;
Juen, Fabian Sebastian;
Kreutz, Christoph;
Micura, Ronald;
Westhof, Eric;
Erlacher, Matthias D

Publication type:

Article

ESRP1 controls biogenesis and function of a large abundant multiexon circRNA.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1387, doi. 10.1093/nar/gkad1138

By:

Liu, Dawei;
Dredge, B Kate;
Bert, Andrew G;
Pillman, Katherine A;
Toubia, John;
Guo, Wenting;
Dyakov, Boris J A;
Migault, Melodie M;
Conn, Vanessa M;
Conn, Simon J;
Gregory, Philip A;
Gingras, Anne-Claude;
Patel, Dinshaw;
Wu, Baixing;
Goodall, Gregory J

Publication type:

Article

Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1359, doi. 10.1093/nar/gkad1134

By:

Decombe, Alice;
Peersen, Olve;
Sutto-Ortiz, Priscila;
Chamontin, Célia;
Piorkowski, Géraldine;
Canard, Bruno;
Nisole, Sébastien;
Decroly, Etienne

Publication type:

Article

MutSβ protects common fragile sites by facilitating homology-directed repair at DNA double-strand breaks with secondary structures.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. 1120, doi. 10.1093/nar/gkad1112

By:

Li, Youhang;
Zhang, Yunkun;
Shah, Sameer Bikram;
Chang, Chia-Yu;
Wang, Hailong;
Wu, Xiaohua

Publication type:

Article