Works matching IS 03051048 AND DT 2023 AND VI 51 AND IP 10

Results: 45

Inferring ligand-receptor cellular networks from bulk and spatial transcriptomic datasets with BulkSignalR.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4726, doi. 10.1093/nar/gkad352

By:

Villemin, Jean-Philippe;
Bassaganyas, Laia;
Pourquier, Didier;
Boissière, Florence;
Cabello-Aguilar, Simon;
Crapez, Evelyne;
Tanos, Rita;
Cornillot, Emmanuel;
Turtoi, Andrei;
Colinge, Jacques

Publication type:

Article

Correction to 'PIDD mediates the association of DNA-pkcs and ATR at stalled replication forks to facilitate the ATR signaling pathway'.

Published in:: 2023
Publication type:: Correction Notice

Discovery and characterization of novel Cre-type tyrosine site-specific recombinases for advanced genome engineering.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5285, doi. 10.1093/nar/gkad366

By:

Jelicic, Milica;
Schmitt, Lukas Theo;
Paszkowski-Rogacz, Maciej;
Walder, Angelika;
Schubert, Nadja;
Hoersten, Jenna;
Sürün, Duran;
Buchholz, Frank

Publication type:

Article

Retraction of 'COUP-TF interacting protein 2 represses the initial phase of HIV-1 gene transcription in human microglial cells'.

Published in:: 2023
Publication type:: Correction Notice

Zinc cluster transcription factors frequently activate target genes using a non-canonical half-site binding mode.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5006, doi. 10.1093/nar/gkad320

By:

Recio, Pamela S;
Mitra, Nikhil J;
Shively, Christian A;
Song, David;
Jaramillo, Grace;
Lewis, Kristine Shady;
Chen, Xuhua;
Mitra, Robi D

Publication type:

Article

Core defense hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4995, doi. 10.1093/nar/gkad317

By:

Johnson, Matthew C;
Laderman, Eric;
Huiting, Erin;
Zhang, Chi;
Davidson, Alan;
Bondy-Denomy, Joseph

Publication type:

Article

Roles of the leader-trailer helix and antitermination complex in biogenesis of the 30S ribosomal subunit.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5242, doi. 10.1093/nar/gkad316

By:

Warner, Benjamin R;
Bundschuh, Ralf;
Fredrick, Kurt

Publication type:

Article

RPA engages telomeric G-quadruplexes more effectively than CST.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5073, doi. 10.1093/nar/gkad315

By:

Olson, Conner L;
Barbour, Alexandra T;
Wieser, Thomas A;
Wuttke, Deborah S

Publication type:

Article

Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5255, doi. 10.1093/nar/gkad314

By:

Godoy, Andre Schutzer;
Nakamura, Aline Minalli;
Douangamath, Alice;
Song, Yun;
Noske, Gabriela Dias;
Gawriljuk, Victor Oliveira;
Fernandes, Rafaela Sachetto;
Pereira, Humberto D Muniz;
Oliveira, Ketllyn Irene Zagato;
Fearon, Daren;
Dias, Alexandre;
Krojer, Tobias;
Fairhead, Michael;
Powell, Alisa;
Dunnet, Louise;
Brandao-Neto, Jose;
Skyner, Rachael;
Chalk, Rod;
Bajusz, Dávid;
Bege, Miklós

Publication type:

Article

Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4713, doi. 10.1093/nar/gkad309

By:

Genna, Vito;
Iglesias-Fernández, Javier;
Reyes-Fraile, Laura;
Villegas, Nuria;
Guckian, Kevin;
Seth, Punit;
Wan, Brad;
Cabrero, Cristina;
Terrazas, Montserrat;
Brun-Heath, Isabelle;
González, Carlos;
Sciabola, Simone;
Villalobos, Anabella;
Orozco, Modesto

Publication type:

Article

Changes in metabolic landscapes shape divergent but distinct mutational signatures and cytotoxic consequences of redox stress.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5056, doi. 10.1093/nar/gkad305

By:

Degtyareva, Natalya P;
Placentra, Victoria C;
Gabel, Scott A;
Klimczak, Leszek J;
Gordenin, Dmitry A;
Wagner, Brett A;
Buettner, Garry R;
Mueller, Geoffrey A;
Smirnova, Tatyana I;
Doetsch, Paul W

Publication type:

Article

Heat shock transcription factors demonstrate a distinct mode of interaction with mitotic chromosomes.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5040, doi. 10.1093/nar/gkad304

By:

Price, Rachel M;
Budzyński, Marek A;
Shen, Junzhou;
Mitchell, Jennifer E;
Kwan, James Z J;
Teves, Sheila S

Publication type:

Article

Phase-separated DropCRISPRa platform for efficient gene activation in mammalian cells and mice.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5271, doi. 10.1093/nar/gkad301

By:

Ma, Shufeng;
Liao, Kaitong;
Li, Mengrao;
Wang, Xinlong;
Lv, Jie;
Zhang, Xin;
Huang, Hongxin;
Li, Lian;
Huang, Tao;
Guo, Xiaohua;
Lin, Ying;
Rong, Zhili

Publication type:

Article

Not4-dependent targeting of MMF1 mRNA to mitochondria limits its expression via ribosome pausing, Egd1 ubiquitination, Caf130, no-go-decay and autophagy.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5022, doi. 10.1093/nar/gkad299

By:

Chen, Siyu;
Allen, George;
Panasenko, Olesya O;
Collart, Martine A

Publication type:

Article

Bacterial Argonaute nucleases reveal different modes of DNA targeting in vitro and in vivo.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5106, doi. 10.1093/nar/gkad290

By:

Lisitskaya, Lidiya;
Kropocheva, Ekaterina;
Agapov, Aleksei;
Prostova, Maria;
Panteleev, Vladimir;
Yudin, Denis;
Ryazansky, Sergei;
Kuzmenko, Anton;
Aravin, Alexei A;
Esyunina, Daria;
Kulbachinskiy, Andrey

Publication type:

Article

GeoBind: segmentation of nucleic acid binding interface on protein surface with geometric deep learning.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. e60, doi. 10.1093/nar/gkad288

By:

Li, Pengpai;
Liu, Zhi-Ping

Publication type:

Article

Sex-lethal regulates back-splicing and generation of the sex-differentially expressed circular RNAs.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5228, doi. 10.1093/nar/gkad280

By:

Fan, Yu-Jie;
Ding, Zhan;
Zhang, Yu;
Su, Ruibao;
Yue, Jia-Le;
Liang, An-Min;
Huang, Qi-Wei;
Meng, Yan-Ran;
Li, Muwang;
Xue, Yuanchao;
Xu, Yong-Zhen

Publication type:

Article

A multidisciplinary approach to the identification of the protein–RNA connectome in double-stranded RNA virus capsids.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5210, doi. 10.1093/nar/gkad274

By:

Sung, Po-yu;
Zhou, Yiyang;
Kao, C Cheng;
Aburigh, Ali A;
Routh, Andrew;
Roy, Polly

Publication type:

Article

A dual gene-specific mutator system installs all transition mutations at similar frequencies in vivo.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. e59, doi. 10.1093/nar/gkad266

By:

Seo, Daeje;
Koh, Bonghyun;
Eom, Ga-eul;
Kim, Hye Won;
Kim, Seokhee

Publication type:

Article

exFINDER: identify external communication signals using single-cell transcriptomics data.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. e58, doi. 10.1093/nar/gkad262

By:

He, Changhan;
Zhou, Peijie;
Nie, Qing

Publication type:

Article

The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5087, doi. 10.1093/nar/gkad261

By:

Schneider, Andy;
Bergsch, Jan;
Lipps, Georg

Publication type:

Article

LncRNA EPR regulates intestinal mucus production and protects against inflammation and tumorigenesis.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5193, doi. 10.1093/nar/gkad257

By:

Briata, Paola;
Mastracci, Luca;
Zapparoli, Ettore;
Caputo, Luca;
Ferracci, Elisa;
Silvestri, Alessandra;
Garuti, Anna;
Hamadou, Meriem Hadjer;
Inga, Alberto;
Marcaccini, Elisa;
Grillo, Federica;
Bucci, Gabriele;
Puri, Pier Lorenzo;
Beznoussenko, Galina;
Mironov, Alexander;
Chiacchiera, Fulvio;
Gherzi, Roberto

Publication type:

Article

Requirement of transcription-coupled nucleotide excision repair for the removal of a specific type of oxidatively induced DNA damage.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4982, doi. 10.1093/nar/gkad256

By:

Sarmini, Leen;
Meabed, Mohammed;
Emmanouil, Eirini;
Atsaves, George;
Robeska, Elena;
Karwowski, Bolesław T;
Campalans, Anna;
Gimisis, Thanasis;
Khobta, Andriy

Publication type:

Article

Efficient reconstruction of cell lineage trees for cell ancestry and cancer.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. e57, doi. 10.1093/nar/gkad254

By:

Jang, Yeongjun;
Fasching, Liana;
Bae, Taejeong;
Tomasini, Livia;
Schreiner, Jeremy;
Szekely, Anna;
Fernandez, Thomas V;
Leckman, James F;
Vaccarino, Flora M;
Abyzov, Alexej

Publication type:

Article

The RNA export factor TbMex67 connects transcription and RNA export in Trypanosoma brucei and sets boundaries for RNA polymerase I.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5177, doi. 10.1093/nar/gkad251

By:

Pozzi, Berta;
Naguleswaran, Arunasalam;
Florini, Francesca;
Rezaei, Zahra;
Roditi, Isabel

Publication type:

Article

Novel mechanisms for the removal of strong replication-blocking HMCES- and thiazolidine-DNA adducts in humans.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4959, doi. 10.1093/nar/gkad246

By:

Sugimoto, Yohei;
Masuda, Yuji;
Iwai, Shigenori;
Miyake, Yumi;
Kanao, Rie;
Masutani, Chikahide

Publication type:

Article

RNA-dependent interactome allows network-based assignment of RNA-binding protein function.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5162, doi. 10.1093/nar/gkad245

By:

Fradera-Sola, Albert;
Nischwitz, Emily;
Bayer, Marie Elisabeth;
Luck, Katja;
Butter, Falk

Publication type:

Article

Insplico: effective computational tool for studying splicing order of adjacent introns genome-wide with short and long RNA-seq reads.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. e56, doi. 10.1093/nar/gkad244

By:

Gohr, André;
Iñiguez, Luis P;
Torres-Méndez, Antonio;
Bonnal, Sophie;
Irimia, Manuel

Publication type:

Article

Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4942, doi. 10.1093/nar/gkad243

By:

D'Augustin, Ostiane;
Gaudon, Virginie;
Siberchicot, Capucine;
Smith, Rebecca;
Chapuis, Catherine;
Depagne, Jordane;
Veaute, Xavier;
Busso, Didier;
Di Guilmi, Anne-Marie;
Castaing, Bertrand;
Radicella, J Pablo;
Campalans, Anna;
Huet, Sébastien

Publication type:

Article

AFM-based force spectroscopy unravels stepwise formation of the DNA transposition complex in the widespread Tn3 family mobile genetic elements.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4929, doi. 10.1093/nar/gkad241

By:

Fernandez, Maricruz;
Shkumatov, Alexander V;
Liu, Yun;
Stulemeijer, Claire;
Derclaye, Sylvie;
Efremov, Rouslan G;
Hallet, Bernard;
Alsteens, David

Publication type:

Article

CTC1 OB-B interaction with TPP1 terminates telomerase and prevents telomere overextension.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4914, doi. 10.1093/nar/gkad237

By:

Wang, Huan;
Ma, Tengfei;
Zhang, Xiaotong;
Chen, Wei;
Lan, Yina;
Kuang, Guotao;
Hsu, Shih-Jui;
He, Zibin;
Chen, Yuxi;
Stewart, Jason;
Bhattacharjee, Anukana;
Luo, Zhenhua;
Price, Carolyn;
Feng, Xuyang

Publication type:

Article

WDR5 is required for DUX4 expression and its pathological effects in FSHD muscular dystrophy.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5144, doi. 10.1093/nar/gkad230

By:

Mocciaro, Emanuele;
Giambruno, Roberto;
Micheloni, Stefano;
Cernilogar, Filippo M;
Andolfo, Annapaola;
Consonni, Cristina;
Pannese, Maria;
Ferri, Giulia;
Runfola, Valeria;
Schotta, Gunnar;
Gabellini, Davide

Publication type:

Article

Esearch3D: propagating gene expression in chromatin networks to illuminate active enhancers.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. e55, doi. 10.1093/nar/gkad229

By:

Heer, Maninder;
Giudice, Luca;
Mengoni, Claudia;
Giugno, Rosalba;
Rico, Daniel

Publication type:

Article

Role of the 5′ end phosphorylation state for small RNA stability and target RNA regulation in bacteria.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 5125, doi. 10.1093/nar/gkad226

By:

Schilder, Alexandra;
Görke, Boris

Publication type:

Article

Oocytes can repair DNA damage during meiosis via a microtubule-dependent recruitment of CIP2A–MDC1–TOPBP1 complex from spindle pole to chromosomes.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4899, doi. 10.1093/nar/gkad213

By:

Leem, Jiyeon;
Kim, Jae-Sung;
Oh, Jeong Su

Publication type:

Article

UV-DDB stimulates the activity of SMUG1 during base excision repair of 5-hydroxymethyl-2'-deoxyuridine moieties.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4881, doi. 10.1093/nar/gkad206

By:

Jang, Sunbok;
Raja, Sripriya J;
Roginskaya, Vera;
Schaich, Matthew A;
Watkins, Simon C;
Van Houten, Bennett

Publication type:

Article

LINE-1 repression in Epstein–Barr virus-associated gastric cancer through viral–host genome interaction.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4867, doi. 10.1093/nar/gkad203

By:

Zhang, Mengyu;
Sun, Weikang;
You, Xiaoxin;
Xu, Dongge;
Wang, Lingling;
Yang, Jingping;
Li, Erguang;
He, Susu

Publication type:

Article

Short tandem repeats are important contributors to silencer elements in T cells.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4845, doi. 10.1093/nar/gkad187

By:

Hussain, Saadat;
Sadouni, Nori;
van Essen, Dominic;
Dao, Lan T M;
Ferré, Quentin;
Charbonnier, Guillaume;
Torres, Magali;
Gallardo, Frederic;
Lecellier, Charles-Henri;
Sexton, Tom;
Saccani, Simona;
Spicuglia, Salvatore

Publication type:

Article

The molecular grammar of protein disorder guiding genome-binding locations.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4831, doi. 10.1093/nar/gkad184

By:

Jonas, Felix;
Carmi, Miri;
Krupkin, Beniamin;
Steinberger, Joseph;
Brodsky, Sagie;
Jana, Tamar;
Barkai, Naama

Publication type:

Article

Spt6 directly interacts with Cdc73 and is required for Paf1 complex occupancy at active genes in Saccharomyces cerevisiae.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4814, doi. 10.1093/nar/gkad180

By:

Ellison, Mitchell A;
Namjilsuren, Sanchirmaa;
Shirra, Margaret K;
Blacksmith, Matthew S;
Schusteff, Rachel A;
Kerr, Eleanor M;
Fang, Fei;
Xiang, Yufei;
Shi, Yi;
Arndt, Karen M

Publication type:

Article

GCNA is a histone binding protein required for spermatogonial stem cell maintenance.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4791, doi. 10.1093/nar/gkad168

By:

Ribeiro, Jonathan;
Crossan, Gerry P

Publication type:

Article

The novel GATA1-interacting protein HES6 is an essential transcriptional cofactor for human erythropoiesis.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4774, doi. 10.1093/nar/gkad167

By:

Wang, Zi;
Wang, Pan;
Zhang, Jieying;
Gong, Han;
Zhang, Xuchao;
Song, Jianhui;
Nie, Ling;
Peng, Yuanliang;
Li, Yanan;
Peng, Hongling;
Cui, Yajuan;
Li, Heng;
Hu, Bin;
Mi, Jun;
Liang, Long;
Liu, Hong;
Zhang, Ji;
Ye, Mao;
Yazdanbakhsh, Karina;
Mohandas, Narla

Publication type:

Article

Symmetric control of sister chromatid cohesion establishment.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4760, doi. 10.1093/nar/gkad146

By:

Zhang, Jiaxin;
Li, Lili;
Miao, Yu;
Liu, Xiaojing;
Sun, Haitao;
Jiang, Meiqian;
Li, Xiaoli;
Li, Zhen;
Liu, Cong;
Liu, Baohua;
Xu, Xingzhi;
Cao, Qinhong;
Hou, Wenya;
Chen, Chunlai;
Lou, Huiqiang

Publication type:

Article

Endogenous retrovirus-derived enhancers confer the transcriptional regulation of human trophoblast syncytialization.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4745, doi. 10.1093/nar/gkad109

By:

Yu, Miao;
Hu, Xiaoqian;
Pan, Zihang;
Du, Cui;
Jiang, Jing;
Zheng, Wanshan;
Cai, Han;
Wang, Yinan;
Deng, Wenbo;
Wang, Haibin;
Lu, Jinhua;
Sun, Ming-an;
Cao, Bin

Publication type:

Article

Negatively charged, intrinsically disordered regions can accelerate target search by DNA-binding proteins.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 10, p. 4701, doi. 10.1093/nar/gkad045

By:

Wang, Xi;
Bigman, Lavi S;
Greenblatt, Harry M;
Yu, Binhan;
Levy, Yaakov;
Iwahara, Junji

Publication type:

Article