Works matching IS 03051048 AND DT 2024 AND VI 52 AND IP 8

Results: 45

Discovery of a polymorphic gene fusion via bottom-up chimeric RNA prediction.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4409, doi. 10.1093/nar/gkae258

By:

Elfman, Justin;
Goins, Lynette;
Heller, Tessa;
Singh, Sandeep;
Wang, Yuh-Hwa;
Li, Hui

Publication type:

Article

Mutation rate heterogeneity at the sub-gene scale due to local DNA hypomethylation.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4393, doi. 10.1093/nar/gkae252

By:

Mas-Ponte, David;
Supek, Fran

Publication type:

Article

Correction to 'POT-3 preferentially binds the terminal DNA-repeat on the telomeric G-overhang'.

Published in:: 2024
Publication type:: Correction Notice

Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4483, doi. 10.1093/nar/gkae240

By:

Ni, Zuyao;
Ahmed, Nujhat;
Nabeel-Shah, Syed;
Guo, Xinghua;
Pu, Shuye;
Song, Jingwen;
Marcon, Edyta;
Burke, Giovanni L;
Tong, Amy Hin Yan;
Chan, Katherine;
Ha, Kevin C H;
Blencowe, Benjamin J;
Moffat, Jason;
Greenblatt, Jack F

Publication type:

Article

Correction to 'SomaMutDB: a database of somatic mutations in normal human tissues'.

Published in:: 2024
Publication type:: Correction Notice

Correction to 'Non-CpG methylation by DNMT3B facilitates REST binding and gene silencing in developing mouse hearts'.

Published in:: 2024
Publication type:: Correction Notice

The effect of pseudoknot base pairing on cotranscriptional structural switching of the fluoride riboswitch.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4466, doi. 10.1093/nar/gkae231

By:

Hertz, Laura M;
White, Elise N;
Kuznedelov, Konstantin;
Cheng, Luyi;
Yu, Angela M;
Kakkaramadam, Rivaan;
Severinov, Konstantin;
Chen, Alan;
Lucks, Julius B

Publication type:

Article

Structure-functional characterization of Lactococcus AbiA phage defense system.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4723, doi. 10.1093/nar/gkae230

By:

Gapińska, Marta;
Zajko, Weronika;
Skowronek, Krzysztof;
Figiel, Małgorzata;
Krawczyk, Paweł S;
Egorov, Artyom A;
Dziembowski, Andrzej;
Johansson, Marcus J O;
Nowotny, Marcin

Publication type:

Article

Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4702, doi. 10.1093/nar/gkae229

By:

Sahoo, Bikash R;
Kocman, Vojč;
Clark, Nathan;
Myers, Nikhil;
Deng, Xiexiong;
Wong, Ee L;
Yang, Harry J;
Kotar, Anita;
Guzman, Bryan B;
Dominguez, Daniel;
Plavec, Janez;
Bardwell, James C A

Publication type:

Article

Multiplexed in-situ mutagenesis driven by a dCas12a-based dual-function base editor.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4739, doi. 10.1093/nar/gkae228

By:

Wu, Yaokang;
Li, Yang;
Liu, Yanfeng;
Xiu, Xiang;
Liu, Jiaheng;
Zhang, Linpei;
Li, Jianghua;
Du, Guocheng;
Lv, Xueqin;
Chen, Jian;
Ledesma-Amaro, Rodrigo;
Liu, Long

Publication type:

Article

ORBIT for E. coli: kilobase-scale oligonucleotide recombineering at high throughput and high efficiency.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. e43, doi. 10.1093/nar/gkae227

By:

Saunders, Scott H;
Ahmed, Ayesha M

Publication type:

Article

Resolving the intricate binding of neomycin B to multiple binding motifs of a neomycin-sensing riboswitch aptamer by native top-down mass spectrometry and NMR spectroscopy.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4691, doi. 10.1093/nar/gkae224

By:

Heel, Sarah Viola;
Juen, Fabian;
Bartosik, Karolina;
Micura, Ronald;
Kreutz, Christoph;
Breuker, Kathrin

Publication type:

Article

Bridging DNA contacts allow Dps from E. coli to condense DNA.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4456, doi. 10.1093/nar/gkae223

By:

Shahu, Sneha;
Vtyurina, Natalia;
Das, Moumita;
Meyer, Anne S;
Ganji, Mahipal;
Abbondanzieri, Elio A

Publication type:

Article

A phage nucleus-associated RNA-binding protein is required for jumbo phage infection.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4440, doi. 10.1093/nar/gkae216

By:

Enustun, Eray;
Armbruster, Emily G;
Lee, Jina;
Zhang, Sitao;
Yee, Brian A;
Malukhina, Kseniya;
Gu, Yajie;
Deep, Amar;
Naritomi, Jack T;
Liang, Qishan;
Aigner, Stefan;
Adler, Benjamin A;
Cress, Brady F;
Doudna, Jennifer A;
Chaikeeratisak, Vorrapon;
Cleveland, Don W;
Ghassemian, Majid;
Bintu, Bogdan;
Yeo, Gene W;
Pogliano, Joe

Publication type:

Article

Unearthing a novel function of SRSF1 in binding and unfolding of RNA G-quadruplexes.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4676, doi. 10.1093/nar/gkae213

By:

De Silva, Naiduwadura Ivon Upekala;
Lehman, Nathan;
Fargason, Talia;
Paul, Trenton;
Zhang, Zihan;
Zhang, Jun

Publication type:

Article

The crystal structure of bacteriophage λ RexA provides novel insights into the DNA binding properties of Rex-like phage exclusion proteins.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4659, doi. 10.1093/nar/gkae212

By:

Adams, Myfanwy C;
Schiltz, Carl J;
Sun, Jing;
Hosford, Christopher J;
Johnson, Virginia M;
Pan, Hao;
Borbat, Peter P;
Freed, Jack H;
Thomason, Lynn C;
Court, Carolyn;
Court, Donald L;
Chappie, Joshua S

Publication type:

Article

Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4137, doi. 10.1093/nar/gkae210

By:

Chen, Nanjun;
Yu, Jixiang;
Liu, Zhe;
Meng, Lingkuan;
Li, Xiangtao;
Wong, Ka-Chun

Publication type:

Article

RNA polymerase SI3 domain modulates global transcriptional pausing and pause-site fluctuations.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4556, doi. 10.1093/nar/gkae209

By:

Bao, Yu;
Cao, Xinyun;
Landick, Robert

Publication type:

Article

BRD2 promotes antibody class switch recombination by facilitating DNA repair in collaboration with NIPBL.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4422, doi. 10.1093/nar/gkae204

By:

Gothwal, Santosh K;
Refaat, Ahmed M;
Nakata, Mikiyo;
Stanlie, Andre;
Honjo, Tasuku;
Begum, Nasim A

Publication type:

Article

txtools: an R package facilitating analysis of RNA modifications, structures, and interactions.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. e42, doi. 10.1093/nar/gkae203

By:

Garcia-Campos, Miguel Angel;
Schwartz, Schraga

Publication type:

Article

Live-cell imaging of human apurinic/apyrimidinic endonuclease 1 in the nucleus and nucleolus using a chaperone@DNA probe.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. e41, doi. 10.1093/nar/gkae202

By:

Cao, Xiangjian;
Zheng, Jinghui;
Zhang, Ruilan;
Sun, Ying;
Zhao, Meiping

Publication type:

Article

The diversity of splicing modifiers acting on A-1 bulged 5′-splice sites reveals rules for rational drug design.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4124, doi. 10.1093/nar/gkae201

By:

Malard, Florian;
Wolter, Antje C;
Marquevielle, Julien;
Morvan, Estelle;
Ecoutin, Agathe;
Rüdisser, Simon H;
Allain, Frédéric H T;
Campagne, Sebastien

Publication type:

Article

Critical steps in the assembly process of the bacterial 50S ribosomal subunit.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4111, doi. 10.1093/nar/gkae199

By:

Seffouh, Amal;
Nikolay, Rainer;
Ortega, Joaquin

Publication type:

Article

Biochemical characterization of the meiosis-essential yet evolutionarily divergent topoisomerase VIB-like protein MTOPVIB from Arabidopsis thaliana.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4541, doi. 10.1093/nar/gkae181

By:

Chen, Hsin-Wen;
Yeh, Hsin-Yi;
Chang, Chih-Chiang;
Kuo, Wei-Chen;
Lin, Sheng-Wei;
Vrielynck, Nathalie;
Grelon, Mathilde;
Chan, Nei-Li;
Chi, Peter

Publication type:

Article

Molecular basis of A. thaliana KEOPS complex in biosynthesizing tRNA t6A.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4523, doi. 10.1093/nar/gkae179

By:

Zheng, Xinxing;
Su, Chenchen;
Duan, Lei;
Jin, Mengqi;
Sun, Yongtao;
Zhu, Li;
Zhang, Wenhua

Publication type:

Article

Determinants of CRISPR Cas12a nuclease activation by DNA and RNA targets.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4502, doi. 10.1093/nar/gkae152

By:

Nalefski, Eric A;
Kooistra, Remy M;
Parikh, Ishira;
Hedley, Samantha;
Rajaraman, Karunya;
Madan, Damian

Publication type:

Article

COSA-1 mediated pro-crossover complex formation promotes meiotic crossing over in C. elegans.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4375, doi. 10.1093/nar/gkae130

By:

Yang, Yuejun;
Wang, Nan;
Liu, Guoteng;
Nan, Wencong;
Wang, Bin;
Gartner, Anton;
Zhang, Hongtao;
Hong, Ye

Publication type:

Article

Pathogenic CANVAS (AAGGG)n repeats stall DNA replication due to the formation of alternative DNA structures.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4361, doi. 10.1093/nar/gkae124

By:

Hisey, Julia A;
Radchenko, Elina A;
Mandel, Nicholas H;
McGinty, Ryan J;
Matos-Rodrigues, Gabriel;
Rastokina, Anastasia;
Masnovo, Chiara;
Ceschi, Silvia;
Hernandez, Alfredo;
Nussenzweig, André;
Mirkin, Sergei M

Publication type:

Article

The origin recognition complex requires chromatin tethering by a hypervariable intrinsically disordered region that is functionally conserved from sponge to man.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4344, doi. 10.1093/nar/gkae122

By:

Adiji, Olubu A;
McConnell, Brendan S;
Parker, Matthew W

Publication type:

Article

Physical interaction with Spo11 mediates the localisation of Mre11 to chromatin in meiosis and promotes its nuclease activity.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4328, doi. 10.1093/nar/gkae111

By:

Aithal, Rakesh;
Nangalia, Kuldeep;
Spirek, Mario;
Chen, Doris;
Klein, Franz;
Krejci, Lumir

Publication type:

Article

DNA-PK controls Apollo's access to leading-end telomeres.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4313, doi. 10.1093/nar/gkae105

By:

Sonmez, Ceylan;
Toia, Beatrice;
Eickhoff, Patrik;
Matei, Andreea Medeea;
El Beyrouthy, Michael;
Wallner, Björn;
Douglas, Max E;
de Lange, Titia;
Lottersberger, Francisca

Publication type:

Article

Novel insights into the role of translesion synthesis polymerase in DNA incorporation and bypass of 5-fluorouracil in colorectal cancer.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4295, doi. 10.1093/nar/gkae102

By:

Averill, Jameson R;
Lin, Jackson C;
Jung, John;
Jung, Hunmin

Publication type:

Article

Phylogeny-linked occurrence of ribosome stalling on the mRNAs of Arabidopsis unfolded protein response factor bZIP60 orthologs in divergent plant species.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4276, doi. 10.1093/nar/gkae101

By:

Imamichi, Tomoya;
Kusumoto, Nao;
Aoyama, Haruka;
Takamatsu, Seidai;
Honda, Yugo;
Muraoka, Shiori;
Hagiwara-Komoda, Yuka;
Chiba, Yukako;
Onouchi, Hitoshi;
Yamashita, Yui;
Naito, Satoshi

Publication type:

Article

Landscape of RNA pseudouridylation in archaeon Sulfolobus islandicus.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4644, doi. 10.1093/nar/gkae096

By:

Li, Yuqian;
Wu, Songlin;
Ye, Keqiong

Publication type:

Article

Zebrafish Mbd5 binds to RNA m5C and regulates histone deubiquitylation and gene expression in development metabolism and behavior.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4257, doi. 10.1093/nar/gkae093

By:

Guo, Jianhua;
Zou, Zhongyu;
Dou, Xiaoyang;
Zhao, Xiang;
Wang, Yimin;
Wei, Liqiang;
Pi, Yan;
Wang, Yi;
He, Chuan;
Guo, Su

Publication type:

Article

Lineage-determining transcription factor-driven promoters regulate cell type-specific macrophage gene expression.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4234, doi. 10.1093/nar/gkae088

By:

Nagy, Gergely;
Bojcsuk, Dóra;
Tzerpos, Petros;
Cseh, Tímea;
Nagy, László

Publication type:

Article

Ribosomal collision is not a prerequisite for ZNF598-mediated ribosome ubiquitination and disassembly of ribosomal complexes by ASCC.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4627, doi. 10.1093/nar/gkae087

By:

Miścicka, Anna;
Bulakhov, Alexander G;
Kuroha, Kazushige;
Zinoviev, Alexandra;
Hellen, Christopher U T;
Pestova, Tatyana V

Publication type:

Article

Leveraging chromatin state transitions for the identification of regulatory networks orchestrating heart regeneration.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4215, doi. 10.1093/nar/gkae085

By:

Cordero, Julio;
Elsherbiny, Adel;
Wang, Yinuo;
Jürgensen, Lonny;
Constanty, Florian;
Günther, Stefan;
Boerries, Melanie;
Heineke, Joerg;
Beisaw, Arica;
Leuschner, Florian;
Hassel, David;
Dobreva, Gergana

Publication type:

Article

Set2 regulates Ccp1 and Swc2 to ensure centromeric stability by retargeting CENP-A.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4198, doi. 10.1093/nar/gkae084

By:

Lim, Kim Kiat;
Lam, Ulysses Tsz Fung;
Li, Ying;
Zeng, Yi Bing;
Yang, Henry;
Chen, Ee Sin

Publication type:

Article

RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4604, doi. 10.1093/nar/gkae081

By:

Vaňková Hausnerová, Viola;
Shoman, Mahmoud;
Kumar, Dilip;
Schwarz, Marek;
Modrák, Martin;
Jirát Matějčková, Jitka;
Mikesková, Eliška;
Neva, Silvia;
Herrmannová, Anna;
Šiková, Michaela;
Halada, Petr;
Novotná, Iva;
Pajer, Petr;
Valášek, Leoš Shivaya;
Převorovský, Martin;
Krásný, Libor;
Hnilicová, Jarmila

Publication type:

Article

Activation of zinc uptake regulator by zinc binding to three regulatory sites.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4185, doi. 10.1093/nar/gkae079

By:

Choi, Yunchan;
Koh, Junseock;
Cha, Sun-Shin;
Roe, Jung-Hye

Publication type:

Article

All exons are not created equal—exon vulnerability determines the effect of exonic mutations on splicing.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4588, doi. 10.1093/nar/gkae077

By:

Holm, Lise L;
Doktor, Thomas K;
Flugt, Katharina K;
Petersen, Ulrika S S;
Petersen, Rikke;
Andresen, Brage S

Publication type:

Article

Temperature-sensitive splicing defects in Arabidopsis mitochondria caused by mutations in the ROOT PRIMORDIUM DEFECTIVE 1 gene.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4575, doi. 10.1093/nar/gkae072

By:

Wang, Chuande;
Quadrado, Martine;
Mireau, Hakim

Publication type:

Article

Differential expression of paralog RNA binding proteins establishes a dynamic splicing program required for normal cerebral cortex development.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4167, doi. 10.1093/nar/gkae071

By:

Cesari, Eleonora;
Farini, Donatella;
Medici, Vanessa;
Ehrmann, Ingrid;
Guerra, Marika;
Testa, Erika;
Naro, Chiara;
Geloso, Maria Concetta;
Pagliarini, Vittoria;
La Barbera, Livia;
D'Amelio, Marcello;
Orsini, Tiziana;
Vecchioli, Stefano Farioli;
Tamagnone, Luca;
Fort, Philippe;
Viscomi, Maria Teresa;
Elliott, David J;
Sette, Claudio

Publication type:

Article

Chromatin damage generated by DNA intercalators leads to degradation of RNA Polymerase II.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 8, p. 4151, doi. 10.1093/nar/gkae069

By:

Espinoza, Jaime A;
Kanellis, Dimitris C;
Saproo, Sheetanshu;
Leal, Karla;
Martinez, Johana Fernandez;
Bartek, Jiri;
Lindström, Mikael S

Publication type:

Article