Works matching IS 03051048 AND DT 2021 AND VI 49 AND IP 9

Results: 44

MoiRNAiFold: a novel tool for complex in silico RNA design.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 4934, doi. 10.1093/nar/gkab331

By:

Minuesa, Gerard;
Alsina, Cristina;
Garcia-Martin, Juan Antonio;
Oliveros, Juan Carlos;
Dotu, Ivan

Publication type:

Article

Activation-induced deaminase is critical for the establishment of DNA methylation patterns prior to the germinal center reaction.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5057, doi. 10.1093/nar/gkab322

By:

Català-Moll, Francesc;
Ferreté-Bonastre, Anna G;
Li, Tianlu;
Weichenhan, Dieter;
Lutsik, Pavlo;
Ciudad, Laura;
Álvarez-Prado, Ángel F;
Rodríguez-Ubreva, Javier;
Klemann, Christian;
Speckmann, Carsten;
Vilas-Zornoza, Amaya;
Abolhassani, Hassan;
Martínez-Gallo, Mónica;
Dieli-Crimi, Romina;
Rivière, Jacques G;
Martín-Nalda, Andrea;
Colobran, Roger;
Soler-Palacín, Pere;
Kracker, Sven;
Hammarström, Lennart

Publication type:

Article

Crystal structure of SARS-CoV-2 nsp10 bound to nsp14-ExoN domain reveals an exoribonuclease with both structural and functional integrity.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5382, doi. 10.1093/nar/gkab320

By:

Lin, Sheng;
Chen, Hua;
Chen, Zimin;
Yang, Fanli;
Ye, Fei;
Zheng, Yue;
Yang, Jing;
Lin, Xi;
Sun, Honglu;
Wang, Lingling;
Wen, Ao;
Dong, Haohao;
Xiao, Qingjie;
Deng, Dong;
Cao, Yu;
Lu, Guangwen

Publication type:

Article

PIN and CCCH Zn-finger domains coordinate RNA targeting in ZC3H12 family endoribonucleases.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5369, doi. 10.1093/nar/gkab316

By:

Garg, Ankur;
Roske, Yvette;
Yamada, Shinnosuke;
Uehata, Takuya;
Takeuchi, Osamu;
Heinemann, Udo

Publication type:

Article

Solution structure(s) of trinucleosomes from contrast variation SAXS.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5028, doi. 10.1093/nar/gkab290

By:

Mauney, Alexander W;
Muthurajan, Uma M;
Luger, Karolin;
Pollack, Lois

Publication type:

Article

Increased expression of tryptophan and tyrosine tRNAs elevates stop codon readthrough of reporter systems in human cell lines.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5202, doi. 10.1093/nar/gkab315

By:

Beznosková, Petra;
Bidou, Laure;
Namy, Olivier;
Valášek, Leoš Shivaya

Publication type:

Article

Folding and persistence times of intramolecular G-quadruplexes transiently embedded in a DNA duplex.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5189, doi. 10.1093/nar/gkab306

By:

Tran, Phong Lan Thao;
Rieu, Martin;
Hodeib, Samar;
Joubert, Alexandra;
Ouellet, Jimmy;
Alberti, Patrizia;
Bugaut, Anthony;
Allemand, Jean-François;
Boulé, Jean-Baptiste;
Croquette, Vincent

Publication type:

Article

ERG transcription factors have a splicing regulatory function involving RBFOX2 that is altered in the EWS-FLI1 oncogenic fusion.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5038, doi. 10.1093/nar/gkab305

By:

Saulnier, Olivier;
Guedri-Idjouadiene, Katia;
Aynaud, Marie-Ming;
Chakraborty, Alina;
Bruyr, Jonathan;
Pineau, Joséphine;
O'Grady, Tina;
Mirabeau, Olivier;
Grossetête, Sandrine;
Galvan, Bartimée;
Claes, Margaux;
Al Oula Hassoun, Zahra;
Sadacca, Benjamin;
Laud, Karine;
Zaïdi, Sakina;
Surdez, Didier;
Baulande, Sylvain;
Rambout, Xavier;
Tirode, Franck;
Dutertre, Martin

Publication type:

Article

Evolving origin-of-transfer sequences on staphylococcal conjugative and mobilizable plasmids—who's mimicking whom?

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5177, doi. 10.1093/nar/gkab303

By:

Yui Eto, Karina;
Kwong, Stephen M;
LaBreck, Patrick T;
Crow, Jade E;
Traore, Daouda A K;
Parahitiyawa, Nipuna;
Fairhurst, Heather M;
Merrell, D Scott;
Firth, Neville;
Bond, Charles S;
Ramsay, Joshua P

Publication type:

Article

Marker-free quantification of repair pathway utilization at Cas9-induced double-strand breaks.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5095, doi. 10.1093/nar/gkab299

By:

Feng, Wanjuan;
Simpson, Dennis A;
Cho, Jang-Eun;
Carvajal-Garcia, Juan;
Smith, Chelsea M;
Headley, Kathryn M;
Hathaway, Nate;
Ramsden, Dale A;
Gupta, Gaorav P

Publication type:

Article

HDAC3 controls male fertility through enzyme-independent transcriptional regulation at the meiotic exit of spermatogenesis.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5106, doi. 10.1093/nar/gkab313

By:

Yin, Huiqi;
Kang, Zhenlong;
Zhang, Yingwen;
Gong, Yingyun;
Liu, Mengrou;
Xue, Yanfeng;
He, Wenxiu;
Wang, Yanfeng;
Zhang, Shuya;
Xu, Qiushi;
Fu, Kaiqiang;
Zheng, Bangjin;
Xie, Jie;
Zhang, Jinwen;
Wang, Yuanyuan;
Lin, Mingyan;
Zhang, Yihan;
Feng, Hua;
Xin, Changpeng;
Guan, Yichun

Publication type:

Article

The human tRNA-guanine transglycosylase displays promiscuous nucleobase preference but strict tRNA specificity.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 4877, doi. 10.1093/nar/gkab289

By:

Fergus, Claire;
Al-qasem, Mashael;
Cotter, Michelle;
McDonnell, Ciara M;
Sorrentino, Emiliano;
Chevot, Franciane;
Hokamp, Karsten;
Senge, Mathias O;
Southern, John M;
Connon, Stephen J;
Kelly, Vincent P

Publication type:

Article

DDX3 depletion represses translation of mRNAs with complex 5′ UTRs.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5336, doi. 10.1093/nar/gkab287

By:

Calviello, Lorenzo;
Venkataramanan, Srivats;
Rogowski, Karol J;
Wyler, Emanuel;
Wilkins, Kevin;
Tejura, Malvika;
Thai, Bao;
Krol, Jacek;
Filipowicz, Witold;
Landthaler, Markus;
Floor, Stephen N

Publication type:

Article

Decoupling the bridge helix of Cas12a results in a reduced trimming activity, increased mismatch sensitivity and impaired conformational transitions.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5278, doi. 10.1093/nar/gkab286

By:

Wörle, Elisabeth;
Jakob, Leonhard;
Schmidbauer, Andreas;
Zinner, Gabriel;
Grohmann, Dina

Publication type:

Article

A unified computational view of DNA duplex, triplex, quadruplex and their donor–acceptor interactions.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 4919, doi. 10.1093/nar/gkab285

By:

Park, Gyuri;
Kang, Byunghwa;
Park, Soyeon V;
Lee, Donghwa;
Oh, Seung Soo

Publication type:

Article

Slow chromatin dynamics enhances promoter accessibility to transcriptional condensates.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5017, doi. 10.1093/nar/gkab275

By:

Yamamoto, Tetsuya;
Sakaue, Takahiro;
Schiessel, Helmut

Publication type:

Article

Mycobacterium tuberculosis Phe-tRNA synthetase: structural insights into tRNA recognition and aminoacylation.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5351, doi. 10.1093/nar/gkab272

By:

Michalska, Karolina;
Jedrzejczak, Robert;
Wower, Jacek;
Chang, Changsoo;
Baragaña, Beatriz;
Gilbert, Ian H;
Forte, Barbara;
Joachimiak, Andrzej

Publication type:

Article

E. coli RNase I exhibits a strong Ca<sup>2+</sup>-dependent inherent double-stranded RNase activity.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5265, doi. 10.1093/nar/gkab284

By:

Grünberg, Sebastian;
Coxam, Baptiste;
Chen, Tien-Hao;
Dai, Nan;
Saleh, Lana;
Corrêa, Ivan R;
Nichols, Nicole M;
Yigit, Erbay

Publication type:

Article

In vivo targets of Salmonella FinO include a FinP-like small RNA controlling copy number of a cohabitating plasmid.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5319, doi. 10.1093/nar/gkab281

By:

El Mouali, Youssef;
Gerovac, Milan;
Mineikaitė, Raminta;
Vogel, Jörg

Publication type:

Article

A nucleotide-sensing endonuclease from the Gabija bacterial defense system.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5216, doi. 10.1093/nar/gkab277

By:

Cheng, Rui;
Huang, Fengtao;
Wu, Hui;
Lu, Xuelin;
Yan, Yan;
Yu, Bingbing;
Wang, Xionglue;
Zhu, Bin

Publication type:

Article

Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5084, doi. 10.1093/nar/gkab276

By:

Yang, Jie;
Horton, John R;
Akdemir, Kadir C;
Li, Jia;
Huang, Yun;
Kumar, Janani;
Blumenthal, Robert M;
Zhang, Xing;
Cheng, Xiaodong

Publication type:

Article

RNase R is associated in a functional complex with the RhpA DEAD-box RNA helicase in Helicobacter pylori.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5249, doi. 10.1093/nar/gkab283

By:

Tejada-Arranz, Alejandro;
Matos, Rute G;
Quentin, Yves;
Bouilloux-Lafont, Maxime;
Galtier, Eloïse;
Briolat, Valérie;
Kornobis, Etienne;
Douché, Thibaut;
Matondo, Mariette;
Arraiano, Cecilia M;
Raynal, Bertrand;
De Reuse, Hilde

Publication type:

Article

DNA polymerase gamma mutations that impair holoenzyme stability cause catalytic subunit depletion.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5230, doi. 10.1093/nar/gkab282

By:

Silva-Pinheiro, Pedro;
Pardo-Hernández, Carlos;
Reyes, Aurelio;
Tilokani, Lisa;
Mishra, Anup;
Cerutti, Raffaele;
Li, Shuaifeng;
Rozsivalova, Dieu-Hien;
Valenzuela, Sebastian;
Dogan, Sukru A;
Peter, Bradley;
Fernández-Silva, Patricio;
Trifunovic, Aleksandra;
Prudent, Julien;
Minczuk, Michal;
Bindoff, Laurence;
Macao, Bertil;
Zeviani, Massimo;
Falkenberg, Maria;
Viscomi, Carlo

Publication type:

Article

Inhibition of DNA replication initiation by silver nanoclusters.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5074, doi. 10.1093/nar/gkab271

By:

Tao, Yu;
Aparicio, Tomas;
Li, Mingqiang;
Leong, Kam W;
Zha, Shan;
Gautier, Jean

Publication type:

Article

HPF1-dependent PARP activation promotes LIG3-XRCC1-mediated backup pathway of Okazaki fragment ligation.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5003, doi. 10.1093/nar/gkab269

By:

Kumamoto, Soichiro;
Nishiyama, Atsuya;
Chiba, Yoshie;
Miyashita, Ryota;
Konishi, Chieko;
Azuma, Yoshiaki;
Nakanishi, Makoto

Publication type:

Article

eIF4E3 forms an active eIF4F complex during stresses (eIF4F<sup>S</sup>) targeting mTOR and re-programs the translatome.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5159, doi. 10.1093/nar/gkab267

By:

Weiss, Benjamin;
Allen, George Edward;
Kloehn, Joachim;
Abid, Karim;
Jaquier-Gubler, Pascale;
Curran, Joseph Alphonsus

Publication type:

Article

Molecular structure, DNA binding mode, photophysical properties and recommendations for use of SYBR Gold.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5143, doi. 10.1093/nar/gkab265

By:

Kolbeck, Pauline J;
Vanderlinden, Willem;
Gemmecker, Gerd;
Gebhardt, Christian;
Lehmann, Martin;
Lak, Aidin;
Nicolaus, Thomas;
Cordes, Thorben;
Lipfert, Jan

Publication type:

Article

Asymmetry in histone rotation in forced unwrapping and force quench rewrapping in a nucleosome.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 4907, doi. 10.1093/nar/gkab263

By:

Reddy, Govardhan;
Thirumalai, D

Publication type:

Article

Estimation of peptide elongation times from ribosome profiling spectra.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5124, doi. 10.1093/nar/gkab260

By:

Pavlov, Michael Y;
Ullman, Gustaf;
Ignatova, Zoya;
Ehrenberg, Måns

Publication type:

Article

Translational accuracy of a tethered ribosome.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5308, doi. 10.1093/nar/gkab259

By:

Fabret, Celine;
Namy, Olivier

Publication type:

Article

Short DNA/RNA heteroduplex oligonucleotide interacting proteins are key regulators of target gene silencing.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 4864, doi. 10.1093/nar/gkab258

By:

Asada, Ken;
Sakaue, Fumika;
Nagata, Tetsuya;
Zhang, Ji-chun;
Yoshida-Tanaka, Kie;
Abe, Aya;
Nawa, Makiko;
Nishina, Kazutaka;
Yokota, Takanori

Publication type:

Article

Structural variation affecting DNA backbone interactions underlies adaptation of B3 DNA binding domains to constraints imposed by protein architecture.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 4989, doi. 10.1093/nar/gkab257

By:

Jia, Haiyan;
Suzuki, Masaharu;
McCarty, Donald R

Publication type:

Article

Topologies of synthetic gene circuit for optimal fold change activation.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5393, doi. 10.1093/nar/gkab253

By:

Litovco, Phyana;
Barger, Natalia;
Li, Ximing;
Daniel, Ramez

Publication type:

Article

Cistrome analysis of YY1 uncovers a regulatory axis of YY1:BRD2/4-PFKP during tumorigenesis of advanced prostate cancer.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 4971, doi. 10.1093/nar/gkab252

By:

Xu, Chenxi;
Tsai, Yi-Hsuan;
Galbo, Phillip M;
Gong, Weida;
Storey, Aaron J;
Xu, Yuemei;
Byrum, Stephanie D;
Xu, Lingfan;
Whang, Young E;
Parker, Joel S;
Mackintosh, Samuel G;
Edmondson, Ricky D;
Tackett, Alan J;
Huang, Jiaoti;
Zheng, Deyou;
Earp, H Shelton;
Wang, Gang Greg;
Cai, Ling

Publication type:

Article

Implication of repeat insertion domains in the trans-activity of the long non-coding RNA ANRIL.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 4954, doi. 10.1093/nar/gkab245

By:

Alfeghaly, Charbel;
Sanchez, Aymeric;
Rouget, Raphael;
Thuillier, Quentin;
Igel-Bourguignon, Valérie;
Marchand, Virginie;
Branlant, Christiane;
Motorin, Yuri;
Behm-Ansmant, Isabelle;
Maenner, Sylvain

Publication type:

Article

Opposite roles of transcription elongation factors Spt4/5 and Elf1 in RNA polymerase II transcription through B-form versus non-B DNA structures.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 4944, doi. 10.1093/nar/gkab240

By:

Xu, Jun;
Chong, Jenny;
Wang, Dong

Publication type:

Article

A ribonuclease III involved in virulence of Mucorales fungi has evolved to cut exclusively single-stranded RNA.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 5294, doi. 10.1093/nar/gkab238

By:

Cánovas-Márquez, José Tomás;
Falk, Sebastian;
Nicolás, Francisco E;
Padmanabhan, Subramanian;
Zapata-Pérez, Rubén;
Sánchez-Ferrer, Álvaro;
Navarro, Eusebio;
Garre, Victoriano

Publication type:

Article

Untangling the crosstalk between BRCA1 and R-loops during DNA repair.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 4848, doi. 10.1093/nar/gkab178

By:

San Martin Alonso, Marta;
Noordermeer, Sylvie M

Publication type:

Article

Repriming DNA synthesis: an intrinsic restart pathway that maintains efficient genome replication.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 4831, doi. 10.1093/nar/gkab176

By:

Bainbridge, Lewis J;
Teague, Rebecca;
Doherty, Aidan J

Publication type:

Article

G-Quadruplexes as pathogenic drivers in neurodegenerative disorders.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 4816, doi. 10.1093/nar/gkab164

By:

Wang, Ernest;
Thombre, Ravi;
Shah, Yajas;
Latanich, Rachel;
Wang, Jiou

Publication type:

Article

microRNA-mediated translation repression through GYF-1 and IFE-4 in C. elegans development.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 4803, doi. 10.1093/nar/gkab162

By:

Mayya, Vinay K;
Flamand, Mathieu N;
Lambert, Alice M;
Jafarnejad, Seyed Mehdi;
Wohlschlegel, James A;
Sonenberg, Nahum;
Duchaine, Thomas F

Publication type:

Article

Independent component analysis based gene co-expression network inference (ICAnet) to decipher functional modules for better single-cell clustering and batch integration.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. e54, doi. 10.1093/nar/gkab089

By:

Wang, Weixu;
Tan, Huanhuan;
Sun, Mingwan;
Han, Yiqing;
Chen, Wei;
Qiu, Shengnu;
Zheng, Ke;
Wei, Gang;
Ni, Ting

Publication type:

Article

Integrating quantitative proteomics with accurate genome profiling of transcription factors by greenCUT&RUN.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. e49, doi. 10.1093/nar/gkab038

By:

Nizamuddin, Sheikh;
Koidl, Stefanie;
Bhuiyan, Tanja;
Werner, Tamara V;
Biniossek, Martin L;
Bonvin, Alexandre M J J;
Lassmann, Silke;
Timmers, HThMarc

Publication type:

Article

A systems-level gene regulatory network model for Plasmodium falciparum.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 9, p. 4891, doi. 10.1093/nar/gkaa1245

By:

Neal, Maxwell L;
Wei, Ling;
Peterson, Eliza;
Arrieta-Ortiz, Mario L;
Danziger, Samuel A;
Baliga, Nitin S;
Kaushansky, Alexis;
Aitchison, John D

Publication type:

Article