Works matching IS 03051048 AND DT 2021 AND VI 49 AND IP 22

Results: 46

MetaPlatanus: a metagenome assembler that combines long-range sequence links and species-specific features.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. e130, doi. 10.1093/nar/gkab831

By:

Kajitani, Rei;
Noguchi, Hideki;
Gotoh, Yasuhiro;
Ogura, Yoshitoshi;
Yoshimura, Dai;
Okuno, Miki;
Toyoda, Atsushi;
Kuwahara, Tomomi;
Hayashi, Tetsuya;
Itoh, Takehiko

Publication type:

Article

RNA-based cooperative protein labeling that permits direct monitoring of the intracellular concentration change of an endogenous protein.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. e132, doi. 10.1093/nar/gkab839

By:

Pe, Kathleen Beverly Alog;
Yatsuzuka, Kenji;
Hakariya, Hayase;
Kida, Tomoki;
Katsuda, Yousuke;
Fukuda, Masatora;
Sato, Shin-ichi

Publication type:

Article

simple and rapid method for enzymatic synthesis of CRISPR-Cas9 sgRNA libraries.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. e131, doi. 10.1093/nar/gkab838

By:

Yates, Joshua D;
Russell, Robert C;
Barton, Nathaniel J;
Yost, H Joseph;
Hill, Jonathon T

Publication type:

Article

BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. e129, doi. 10.1093/nar/gkab829

By:

Li, Hong-Liang;
Pang, Yi-He;
Liu, Bin

Publication type:

Article

Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. e128, doi. 10.1093/nar/gkab824

By:

Tang, Kaihao;
Wang, Weiquan;
Sun, Yamin;
Zhou, Yiqing;
Wang, Pengxia;
Guo, Yunxue;
Wang, Xiaoxue

Publication type:

Article

MLG: multilayer graph clustering for multi-condition scRNA-seq data.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. e127, doi. 10.1093/nar/gkab823

By:

Lu, Shan;
Conn, Daniel J;
Chen, Shuyang;
Johnson, Kirby D;
Bresnick, Emery H;
Keleş, Sündüz

Publication type:

Article

Mapping yeast mitotic 5′ resection at base resolution reveals the sequence and positional dependence of nucleases in vivo.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12607, doi. 10.1093/nar/gkab597

By:

Bazzano, Dominic;
Lomonaco, Stephanie;
Wilson, Thomas E

Publication type:

Article

Cytosine base modifications regulate DNA duplex stability and metabolism.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12870, doi. 10.1093/nar/gkab509

By:

Rausch, Cathia;
Zhang, Peng;
Casas-Delucchi, Corella S;
Daiß, Julia L;
Engel, Christoph;
Coster, Gideon;
Hastert, Florian D;
Weber, Patrick;
Cardoso, M Cristina

Publication type:

Article

Dynamic queuosine changes in tRNA couple nutrient levels to codon choice in Trypanosoma brucei.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12986, doi. 10.1093/nar/gkab1204

By:

Dixit, Sameer;
Kessler, Alan C;
Henderson, Jeremy;
Pan, Xiaobei;
Zhao, Ruoxia;
D'Almeida, Gabriel Silveira;
Kulkarni, Sneha;
Rubio, Mary Anne T;
Hegedűsová, Eva;
Ross, Robert L;
Limbach, Patrick A;
Green, Brian D;
Paris, Zdeněk;
Alfonzo, Juan D

Publication type:

Article

Perinuclear positioning of endosomes can affect PS-ASO activities.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12970, doi. 10.1093/nar/gkab1198

By:

Liang, Xue-hai;
Nichols, Joshua G;
Tejera, Dario;
Crooke, Stanley T

Publication type:

Article

Functional role and ribosomal position of the unique N-terminal region of DHX29, a factor required for initiation on structured mammalian mRNAs.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12955, doi. 10.1093/nar/gkab1192

By:

Sweeney, Trevor R;
Dhote, Vidya;
Guca, Ewelina;
Hellen, Christopher U T;
Hashem, Yaser;
Pestova, Tatyana V

Publication type:

Article

Specificity and sensitivity of an RNA targeting type III CRISPR complex coupled with a NucC endonuclease effector.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 13122, doi. 10.1093/nar/gkab1190

By:

Grüschow, Sabine;
Adamson, Catherine S;
White, Malcolm F

Publication type:

Article

FARS2 deficiency in Drosophila reveals the developmental delay and seizure manifested by aberrant mitochondrial tRNA metabolism.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 13108, doi. 10.1093/nar/gkab1187

By:

Fan, Wenlu;
Jin, Xiaoye;
Xu, Man;
Xi, Yongmei;
Lu, Weiguo;
Yang, Xiaohang;
Guan, Min-Xin;
Ge, Wanzhong

Publication type:

Article

Loss of MED12 activates the TGFβ pathway to promote chemoresistance and replication fork stability in BRCA-deficient cells.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12855, doi. 10.1093/nar/gkab1184

By:

Jackson, Lindsey M;
Dhoonmoon, Ashna;
Hale, Anastasia;
Dennis, Kady A;
Schleicher, Emily M;
Nicolae, Claudia M;
Moldovan, George-Lucian

Publication type:

Article

Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 13092, doi. 10.1093/nar/gkab1180

By:

Rafiee, Mahmoud-Reza;
Zagalak, Julian A;
Sidorov, Sviatoslav;
Steinhauser, Sebastian;
Davey, Karen;
Ule, Jernej;
Luscombe, Nicholas M

Publication type:

Article

Single-molecule mitochondrial DNA sequencing shows no evidence of CpG methylation in human cells and tissues.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12757, doi. 10.1093/nar/gkab1179

By:

Bicci, Iacopo;
Calabrese, Claudia;
Golder, Zoe J;
Gomez-Duran, Aurora;
Chinnery, Patrick F

Publication type:

Article

Zippered G-quadruplex/hemin DNAzyme: exceptional catalyst for universal bioanalytical applications.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 13031, doi. 10.1093/nar/gkab1178

By:

Li, Jia;
Wu, Haiping;
Yan, Yurong;
Yuan, Taixian;
Shu, Yue;
Gao, Xin;
Zhang, Lu;
Li, Siqiao;
Ding, Shijia;
Cheng, Wei

Publication type:

Article

Complexities in the role of acetylation dynamics in modifying inducible gene activation parameters.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12744, doi. 10.1093/nar/gkab1176

By:

Carrera, Samantha;
O'Donnell, Amanda;
Li, Yaoyong;
Nowicki-Osuch, Karol;
Yang, Shen-Hsi;
Baker, Syed Murtuza;
Spiller, David;
Sharrocks, Andrew D

Publication type:

Article

archaeal histone-like protein regulates gene expression in response to salt stress.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12732, doi. 10.1093/nar/gkab1175

By:

Sakrikar, Saaz;
Schmid, Amy K

Publication type:

Article

Structure of CRL2Lrr1, the E3 ubiquitin ligase that promotes DNA replication termination in vertebrates.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 13194, doi. 10.1093/nar/gkab1174

By:

Zhou, Haixia;
Zaher, Manal S;
Walter, Johannes C;
Brown, Alan

Publication type:

Article

Cockayne syndrome group B protein regulates fork restart, fork progression and MRE11-dependent fork degradation in BRCA1/2-deficient cells.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12836, doi. 10.1093/nar/gkab1173

By:

Batenburg, Nicole L;
Mersaoui, Sofiane Y;
Walker, John R;
Coulombe, Yan;
Hammond-Martel, Ian;
Wurtele, Hugo;
Masson, Jean-Yves;
Zhu, Xu-Dong

Publication type:

Article

Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12943, doi. 10.1093/nar/gkab1172

By:

Carmody, Patrick J;
Zimmer, Matthew H;
Kuntz, Charles P;
Harrington, Haley R;
Duckworth, Kate E;
Penn, Wesley D;
Mukhopadhyay, Suchetana;
Miller, Thomas F;
Schlebach, Jonathan P

Publication type:

Article

Negative feedback for DARS2–Fis complex by ATP–DnaA supports the cell cycle-coordinated regulation for chromosome replication.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12820, doi. 10.1093/nar/gkab1171

By:

Miyoshi, Kenya;
Tatsumoto, Yuka;
Ozaki, Shogo;
Katayama, Tsutomu

Publication type:

Article

Dynamic bulge nucleotides in the KSHV PAN ENE triple helix provide a unique binding platform for small molecule ligands.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 13179, doi. 10.1093/nar/gkab1170

By:

Swain, Monalisa;
Ageeli, Abeer A;
Kasprzak, Wojciech K;
Li, Mi;
Miller, Jennifer T;
Sztuba-Solinska, Joanna;
Schneekloth, John S;
Koirala, Deepak;
Piccirili, Joseph;
Fraboni, Americo J;
Murelli, Ryan P;
Wlodawer, Alexander;
Shapiro, Bruce A;
Baird, Nathan;
Le Grice, Stuart F J

Publication type:

Article

Division of labor between SOS and PafBC in mycobacterial DNA repair and mutagenesis.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12805, doi. 10.1093/nar/gkab1169

By:

Adefisayo, Oyindamola O;
Dupuy, Pierre;
Nautiyal, Astha;
Bean, James M;
Glickman, Michael S

Publication type:

Article

DNA methylation variation along the cancer epigenome and the identification of novel epigenetic driver events.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12692, doi. 10.1093/nar/gkab1167

By:

Heery, Richard;
Schaefer, Martin H

Publication type:

Article

BrdU immuno-tagged G-quadruplex ligands: a new ligand-guided immunofluorescence approach for tracking G-quadruplexes in cells.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12644, doi. 10.1093/nar/gkab1166

By:

Masson, Thibaut;
Landras Guetta, Corinne;
Laigre, Eugénie;
Cucchiarini, Anne;
Duchambon, Patricia;
Teulade-Fichou, Marie-Paule;
Verga, Daniela

Publication type:

Article

Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 13165, doi. 10.1093/nar/gkab1162

By:

Carroll, Brittany L;
Zahn, Karl E;
Hanley, John P;
Wallace, Susan S;
Dragon, Julie A;
Doublié, Sylvie

Publication type:

Article

Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease E reveals insights into its function and substrate recognition.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 13075, doi. 10.1093/nar/gkab1161

By:

Hoffmann, Ute A;
Heyl, Florian;
Rogh, Said N;
Wallner, Thomas;
Backofen, Rolf;
Hess, Wolfgang R;
Steglich, Claudia;
Wilde, Annegret

Publication type:

Article

SARS-CoV-2 RNA polymerase is a viral RNA capping enzyme.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 13019, doi. 10.1093/nar/gkab1160

By:

Walker, Alexander P;
Fan, Haitian;
Keown, Jeremy R;
Knight, Michael L;
Grimes, Jonathan M;
Fodor, Ervin

Publication type:

Article

Decoding the effects of synonymous variants.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12673, doi. 10.1093/nar/gkab1159

By:

Zeng, Zishuo;
Aptekmann, Ariel A;
Bromberg, Yana

Publication type:

Article

Phosphorylation of ribosomal protein S6 differentially affects mRNA translation based on ORF length.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 13062, doi. 10.1093/nar/gkab1157

By:

Bohlen, Jonathan;
Roiuk, Mykola;
Teleman, Aurelio A

Publication type:

Article

VID22 counteracts G-quadruplex-induced genome instability.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12785, doi. 10.1093/nar/gkab1156

By:

Galati, Elena;
Bosio, Maria C;
Novarina, Daniele;
Chiara, Matteo;
Bernini, Giulia M;
Mozzarelli, Alessandro M;
García-Rubio, Maria L;
Gómez-González, Belén;
Aguilera, Andrés;
Carzaniga, Thomas;
Todisco, Marco;
Bellini, Tommaso;
Nava, Giulia M;
Frigè, Gianmaria;
Sertic, Sarah;
Horner, David S;
Baryshnikova, Anastasia;
Manzari, Caterina;
D'Erchia, Anna M;
Pesole, Graziano

Publication type:

Article

Elongating RNA polymerase II and RNA:DNA hybrids hinder fork progression and gene expression at sites of head-on replication-transcription collisions.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12769, doi. 10.1093/nar/gkab1146

By:

Zardoni, Luca;
Nardini, Eleonora;
Brambati, Alessandra;
Lucca, Chiara;
Choudhary, Ramveer;
Loperfido, Federica;
Sabbioneda, Simone;
Liberi, Giordano

Publication type:

Article

Regulation of PDGFR-β gene expression by targeting the G-vacancy bearing G-quadruplex in promoter.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12634, doi. 10.1093/nar/gkab1154

By:

Chen, Juan-nan;
He, Yi-de;
Liang, Hui-ting;
Cai, Ting-ting;
Chen, Qi;
Zheng, Ke-wei

Publication type:

Article

distinct complex of PRP19-related and trypanosomatid-specific proteins is required for pre-mRNA splicing in trypanosomes.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12929, doi. 10.1093/nar/gkab1152

By:

Srivastava, Ankita;
Ambrósio, Daniela L;
Tasak, Monika;
Gosavi, Ujwala;
Günzl, Arthur

Publication type:

Article

Mechanisms of distinctive mismatch tolerance between Rad51 and Dmc1 in homologous recombination.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 13135, doi. 10.1093/nar/gkab1141

By:

Xu, Jingfei;
Zhao, Lingyun;
Peng, Sijia;
Chu, Huiying;
Liang, Rui;
Tian, Meng;
Connell, Philip P;
Li, Guohui;
Chen, Chunlai;
Wang, Hong-Wei

Publication type:

Article

Position 34 of tRNA is a discriminative element for m5C38 modification by human DNMT2.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 13045, doi. 10.1093/nar/gkab1148

By:

Huang, Zhi-Xuan;
Li, Jing;
Xiong, Qing-Ping;
Li, Hao;
Wang, En-Duo;
Liu, Ru-Juan

Publication type:

Article

Chromosome segregation in Archaea: SegA– and SegB–DNA complex structures provide insights into segrosome assembly.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 13150, doi. 10.1093/nar/gkab1155

By:

Yen, Cheng-Yi;
Lin, Min-Guan;
Chen, Bo-Wei;
Ng, Irene W;
Read, Nicholas;
Kabli, Azhar F;
Wu, Che-Ting;
Shen, Yo-You;
Chen, Chen-Hao;
Barillà, Daniela;
Sun, Yuh-Ju;
Hsiao, Chwan-Deng

Publication type:

Article

CoCoNet—boosting RNA contact prediction by convolutional neural networks.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12661, doi. 10.1093/nar/gkab1144

By:

Zerihun, Mehari B;
Pucci, Fabrizio;
Schug, Alexander

Publication type:

Article

TIN2 is an architectural protein that facilitates TRF2-mediated trans- and cis-interactions on telomeric DNA.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 13000, doi. 10.1093/nar/gkab1142

By:

Kaur, Parminder;
Barnes, Ryan;
Pan, Hai;
Detwiler, Ariana C;
Liu, Ming;
Mahn, Chelsea;
Hall, Jonathan;
Messenger, Zach;
You, Changjiang;
Piehler, Jacob;
Smart, Robert C;
Riehn, Robert;
Opresko, Patricia L;
Wang, Hong

Publication type:

Article

Constrained peptides mimic a viral suppressor of RNA silencing.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12622, doi. 10.1093/nar/gkab1149

By:

Kuepper, Arne;
McLoughlin, Niall M;
Neubacher, Saskia;
Yeste-Vázquez, Alejandro;
Collado Camps, Estel;
Nithin, Chandran;
Mukherjee, Sunandan;
Bethge, Lucas;
Bujnicki, Janusz M;
Brock, Roland;
Heinrichs, Stefan;
Grossmann, Tom N

Publication type:

Article

Controlled RISC loading efficiency of miR168 defined by miRNA duplex structure adjusts ARGONAUTE1 homeostasis.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12912, doi. 10.1093/nar/gkab1138

By:

Dalmadi, Ágnes;
Miloro, Fabio;
Bálint, Jeannette;
Várallyay, Éva;
Havelda, Zoltán

Publication type:

Article

set of accessible enhancers enables the initial response of breast cancer cells to physiological progestin concentrations.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12716, doi. 10.1093/nar/gkab1125

By:

Zaurin, Roser;
Ferrari, Roberto;
Nacht, Ana Silvina;
Carbonell, Jose;
Le Dily, Francois;
Font-Mateu, Jofre;
de Llobet Cucalon, Lara Isabel;
Vidal, Enrique;
Lioutas, Antonios;
Beato, Miguel;
Vicent, Guillermo P

Publication type:

Article

MLL1 is regulated by KSHV LANA and is important for virus latency.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12895, doi. 10.1093/nar/gkab1094

By:

Tan, Min;
Li, Shijun;
Juillard, Franceline;
Chitas, Rute;
Custódio, Tânia F;
Xue, Han;
Szymula, Agnieszka;
Sun, Qiming;
Liu, Bing;
Álvarez, Ángel L;
Chen, She;
Huang, Jing;
Simas, J Pedro;
McVey, Colin E;
Kaye, Kenneth M

Publication type:

Article

Inhibitor of growth protein 3 epigenetically silences endogenous retroviral elements and prevents innate immune activation.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 22, p. 12706, doi. 10.1093/nar/gkab1070

By:

Song, Yanhua;
Hou, Gaopeng;
Diep, Jonathan;
Ooi, Yaw Shin;
Akopyants, Natalia S;
Beverley, Stephen M;
Carette, Jan E;
Greenberg, Harry B;
Ding, Siyuan

Publication type:

Article