Works matching IS 03051048 AND DT 2019 AND VI 47 AND IP 19

Results: 45

Signatures of cell death and proliferation in perturbation transcriptomics data—from confounding factor to effective prediction.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10010, doi. 10.1093/nar/gkz805

By:

Szalai, Bence;
Subramanian, Vigneshwari;
Holland, Christian H;
Alföldi, Róbert;
Puskás, László G;
Saez-Rodriguez, Julio

Publication type:

Article

Molecular determinants for enzalutamide-induced transcription in prostate cancer.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10104, doi. 10.1093/nar/gkz790

By:

Yuan, Fuwen;
Hankey, William;
Wu, Dayong;
Wang, Hongyan;
Somarelli, Jason;
Armstrong, Andrew J;
Huang, Jiaoti;
Chen, Zhong;
Wang, Qianben

Publication type:

Article

The hRPC62 subunit of human RNA polymerase III displays helicase activity.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10313, doi. 10.1093/nar/gkz788

By:

Ayoubi, Leyla El;
Dumay-Odelot, Hélène;
Chernev, Aleksandar;
Boissier, Fanny;
Minvielle-Sébastia, Lionel;
Urlaub, Henning;
Fribourg, Sébastien;
Teichmann, Martin

Publication type:

Article

The internal interaction in RBBP5 regulates assembly and activity of MLL1 methyltransferase complex.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10426, doi. 10.1093/nar/gkz819

By:

Han, Jianming;
Li, Tingting;
Li, Yanjing;
Li, Muchun;
Wang, Xiaoman;
Peng, Chao;
Su, Chen;
Li, Na;
Li, Yiwen;
Xu, Ying;
Chen, Yong

Publication type:

Article

Interbase FRET in RNA: from A to Z.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 9990, doi. 10.1093/nar/gkz812

By:

Füchtbauer, Anders F;
Wranne, Moa S;
Bood, Mattias;
Weis, Erik;
Pfeiffer, Pauline;
Nilsson, Jesper R;
Dahlén, Anders;
Grøtli, Morten;
Wilhelmsson, L Marcus

Publication type:

Article

The metabolic sensor PASK is a histone 3 kinase that also regulates H3K4 methylation by associating with H3K4 MLL2 methyltransferase complex.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10086, doi. 10.1093/nar/gkz786

By:

Karakkat, Jimsheena V;
Kaimala, Suneesh;
Sreedharan, Sreejisha P;
Jayaprakash, Princy;
Adeghate, Ernest A;
Ansari, Suraiya A;
Guccione, Ernesto;
Mensah-Brown, Eric P K;
Starling Emerald, Bright

Publication type:

Article

Oxazinomycin arrests RNA polymerase at the polythymidine sequences.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10296, doi. 10.1093/nar/gkz782

By:

Prajapati, Ranjit K;
Rosenqvist, Petja;
Palmu, Kaisa;
Mäkinen, Janne J;
Malinen, Anssi M;
Virta, Pasi;
Metsä-Ketelä, Mikko;
Belogurov, Georgiy A

Publication type:

Article

Synthetic metabolic computation in a bioluminescence-sensing system.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10464, doi. 10.1093/nar/gkz807

By:

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

Publication type:

Article

Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10027, doi. 10.1093/nar/gkz781

By:

Shulman, Eldad David;
Elkon, Ran

Publication type:

Article

The nuclear structural protein NuMA is a negative regulator of 53BP1 in DNA double-strand break repair.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10475, doi. 10.1093/nar/gkz802

By:

Moreno, Naike Salvador;
Liu, Jing;
Haas, Karen M;
Parker, Laurie L;
Chakraborty, Chaitali;
Kron, Stephen J;
Hodges, Kurt;
Miller, Lance D;
Langefeld, Carl;
Robinson, Paul J;
Lelièvre, Sophie A;
Vidi, Pierre-Alexandre

Publication type:

Article

Ash2l interacts with Oct4-stemness circuitry to promote super-enhancer-driven pluripotency network.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10115, doi. 10.1093/nar/gkz801

By:

Tsai, Ping-Hsing;
Chien, Yueh;
Wang, Mong-Lien;
Hsu, Chih-Hung;
Laurent, Benoit;
Chou, Shih-Jie;
Chang, Wei-Chao;
Chien, Chian-Shiu;
Li, Hsin-Yang;
Lee, Hsin-Chen;
Huo, Teh-Ia;
Hung, Jui-Hung;
Chen, Chung-Hsuan;
Chiou, Shih-Hwa

Publication type:

Article

G-quadruplex located in the 5′UTR of the BAG-1 mRNA affects both its cap-dependent and cap-independent translation through global secondary structure maintenance.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10247, doi. 10.1093/nar/gkz777

By:

Jodoin, Rachel;
Carrier, Julie C;
Rivard, Nathalie;
Bisaillon, Martin;
Perreault, Jean-Pierre

Publication type:

Article

Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8–17 DNAzyme in solution.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10282, doi. 10.1093/nar/gkz773

By:

Ekesan, Şölen;
York, Darrin M

Publication type:

Article

De novo design of programmable inducible promoters.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10452, doi. 10.1093/nar/gkz772

By:

Liu, Xiangyang;
Gupta, Sanjan T P;
Bhimsaria, Devesh;
Reed, Jennifer L;
Rodríguez-Martínez, José A;
Ansari, Aseem Z;
Raman, Srivatsan

Publication type:

Article

Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10414, doi. 10.1093/nar/gkz770

By:

Seffouh, Amal;
Jain, Nikhil;
Jahagirdar, Dushyant;
Basu, Kaustuv;
Razi, Aida;
Ni, Xiaodan;
Guarné, Alba;
Britton, Robert A;
Ortega, Joaquin

Publication type:

Article

SLX4IP acts with SLX4 and XPF–ERCC1 to promote interstrand crosslink repair.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10181, doi. 10.1093/nar/gkz769

By:

Zhang, Huimin;
Chen, Zhen;
Ye, Yin;
Ye, Zu;
Cao, Dan;
Xiong, Yun;
Srivastava, Mrinal;
Feng, Xu;
Tang, Mengfan;
Wang, Chao;
Tainer, John A;
Chen, Junjie

Publication type:

Article

HIF-transcribed p53 chaperones HIF-1α.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10212, doi. 10.1093/nar/gkz766

By:

Madan, Esha;
Parker, Taylor M;
Pelham, Christopher J;
Palma, Antonio M;
Peixoto, Maria L;
Nagane, Masaki;
Chandaria, Aliya;
Tomás, Ana R;
Canas-Marques, Rita;
Henriques, Vanessa;
Galzerano, Antonio;
Cabral-Teixeira, Joaquim;
Selvendiran, Karuppaiyah;
Kuppusamy, Periannan;
Carvalho, Carlos;
Beltran, Antonio;
Moreno, Eduardo;
Pati, Uttam K;
Gogna, Rajan

Publication type:

Article

Multiple cytosolic DNA sensors bind plasmid DNA after transfection.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10235, doi. 10.1093/nar/gkz768

By:

Semenova, Nina;
Bosnjak, Masa;
Markelc, Bostjan;
Znidar, Katarina;
Cemazar, Maja;
Heller, Loree

Publication type:

Article

Human mitochondrial DNA is extensively methylated in a non-CpG context.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10072, doi. 10.1093/nar/gkz762

By:

Patil, Vibha;
Cuenin, Cyrille;
Chung, Felicia;
Aguilera, Jesus R Rodriguez;
Fernandez-Jimenez, Nora;
Romero-Garmendia, Irati;
Bilbao, Jose Ramon;
Cahais, Vincent;
Rothwell, Joseph;
Herceg, Zdenko

Publication type:

Article

mTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10373, doi. 10.1093/nar/gkz761

By:

Chang, Jae-Woong;
Yeh, Hsin-Sung;
Park, Meeyeon;
Erber, Luke;
Sun, Jiao;
Cheng, Sze;
Bui, Alexander M;
Fahmi, Naima Ahmed;
Nasti, Ryan;
Kuang, Rui;
Chen, Yue;
Zhang, Wei;
Yong, Jeongsik

Publication type:

Article

Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10400, doi. 10.1093/nar/gkz760

By:

Pavelich, Ian J;
Maehigashi, Tatsuya;
Hoffer, Eric D;
Ruangprasert, Ajchareeya;
Miles, Stacey J;
Dunham, Christine M

Publication type:

Article

Conserved HORMA domain-containing protein Hop1 stabilizes interaction between proteins of meiotic DNA break hotspots and chromosome axis.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10166, doi. 10.1093/nar/gkz754

By:

Kariyazono, Ryo;
Oda, Arisa;
Yamada, Takatomi;
Ohta, Kunihiro

Publication type:

Article

LYAR potentiates rRNA synthesis by recruiting BRD2/4 and the MYST-type acetyltransferase KAT7 to rDNA.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10357, doi. 10.1093/nar/gkz747

By:

Izumikawa, Keiichi;
Ishikawa, Hideaki;
Yoshikawa, Harunori;
Fujiyama, Sally;
Watanabe, Akira;
Aburatani, Hiroyuki;
Tachikawa, Hiroyuki;
Hayano, Toshiya;
Miura, Yutaka;
Isobe, Toshiaki;
Simpson, Richard J;
Li, Li;
Min, Jinrong;
Takahashi, Nobuhiro

Publication type:

Article

Gene silencing by double-stranded RNA from C. elegans neurons reveals functional mosaicism of RNA interference.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10059, doi. 10.1093/nar/gkz748

By:

Ravikumar, Snusha;
Devanapally, Sindhuja;
Jose, Antony M

Publication type:

Article

Spacer acquisition from RNA mediated by a natural reverse transcriptase-Cas1 fusion protein associated with a type III-D CRISPR–Cas system in Vibrio vulnificus.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10202, doi. 10.1093/nar/gkz746

By:

González-Delgado, Alejandro;
Mestre, Mario Rodríguez;
Martínez-Abarca, Francisco;
Toro, Nicolás

Publication type:

Article

DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. e122, doi. 10.1093/nar/gkz717

By:

Viswanathan, Ramya;
Cheruba, Elsie;
Cheow, Lih Feng

Publication type:

Article

Fail-safe genetic codes designed to intrinsically contain engineered organisms.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10439, doi. 10.1093/nar/gkz745

By:

Calles, Jonathan;
Justice, Isaac;
Brinkley, Detravious;
Garcia, Alexa;
Endy, Drew

Publication type:

Article

Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10388, doi. 10.1093/nar/gkz744

By:

Wang, Na;
Bao, Hongyu;
Chen, Liu;
Liu, Yanhong;
Li, Yue;
Wu, Baixing;
Huang, Hongda

Publication type:

Article

Hypertension-associated mitochondrial DNA 4401A>G mutation caused the aberrant processing of tRNA<sup>Met</sup>, all 8 tRNAs and ND6 mRNA in the light-strand transcript.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10340, doi. 10.1093/nar/gkz742

By:

Zhao, Xiaoxu;
Cui, Limei;
Xiao, Yun;
Mao, Qin;
Aishanjiang, Maerhaba;
Kong, Wanzhong;
Liu, Yuqi;
Chen, Hong;
Hong, Fang;
Jia, Zidong;
Wang, Meng;
Jiang, Pingping;
Guan, Min-Xin

Publication type:

Article

Genome reading by the NF-κB transcription factors.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 9967, doi. 10.1093/nar/gkz739

By:

Mulero, Maria Carmen;
Wang, Vivien Ya-Fan;
Huxford, Tom;
Ghosh, Gourisankar

Publication type:

Article

The human Shu complex functions with PDS5B and SPIDR to promote homologous recombination.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10151, doi. 10.1093/nar/gkz738

By:

Martino, Julieta;
Brunette, Gregory J;
Barroso-González, Jonathan;
Moiseeva, Tatiana N;
Smith, Chelsea M;
Bakkenist, Christopher J;
O'Sullivan, Roderick J;
Bernstein, Kara A

Publication type:

Article

METTL15 introduces N4-methylcytidine into human mitochondrial 12S rRNA and is required for mitoribosome biogenesis.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10267, doi. 10.1093/nar/gkz735

By:

Haute, Lindsey Van;
Hendrick, Alan G;
D'Souza, Aaron R;
Powell, Christopher A;
Rebelo-Guiomar, Pedro;
Harbour, Michael E;
Ding, Shujing;
Fearnley, Ian M;
Andrews, Byron;
Minczuk, Michal

Publication type:

Article

Functional analysis of Cwc24 ZF-domain in 5′ splice site selection.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10327, doi. 10.1093/nar/gkz733

By:

Wu, Nan-Ying;
Cheng, Soo-Chen

Publication type:

Article

Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 9998, doi. 10.1093/nar/gkz730

By:

Ntountoumi, Chrysa;
Vlastaridis, Panayotis;
Mossialos, Dimitris;
Stathopoulos, Constantinos;
Iliopoulos, Ioannis;
Promponas, Vasilios;
Oliver, Stephen G;
Amoutzias, Grigoris D

Publication type:

Article

Post-transcriptional negative feedback regulation of proteostasis through the Dis3 ribonuclease and its disruption by polyQ-expanded Huntingtin.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10040, doi. 10.1093/nar/gkz722

By:

Kong, Ka-Yiu Edwin;
Hung, Ting-Ngai Felix;
Man, Pui-Hei Marcus;
Wong, Tin-Ning;
Cheng, Tao;
Jin, Dong-Yan

Publication type:

Article

A transient reporter for editing enrichment (TREE) in human cells.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. e120, doi. 10.1093/nar/gkz713

By:

Standage-Beier, Kylie;
Tekel, Stefan J;
Brookhouser, Nicholas;
Schwarz, Grace;
Nguyen, Toan;
Wang, Xiao;
Brafman, David A

Publication type:

Article

Efficient inhibition of RNA self-primed extension by addition of competing 3′-capture DNA-improved RNA synthesis by T7 RNA polymerase.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. e118, doi. 10.1093/nar/gkz700

By:

Gholamalipour, Yasaman;
Johnson, William C;
Martin, Craig T

Publication type:

Article

Global prediction of chromatin accessibility using small-cell-number and single-cell RNA-seq.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. e121, doi. 10.1093/nar/gkz716

By:

Zhou, Weiqiang;
Ji, Zhicheng;
Fang, Weixiang;
Ji, Hongkai

Publication type:

Article

Polymerization retardation isothermal amplification (PRIA): a strategy enables sensitively quantify genome-wide 5-methylcytosine oxides rapidly on handy instruments with nanoscale sample input.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. e119, doi. 10.1093/nar/gkz704

By:

Chen, Danping;
Wang, Yang;
Mo, Mingming;
Zhang, Junjie;
Zhang, Yanfei;
Xu, Yuzhi;
Liu, Si-Yang;
Chen, Jun;
Ma, Yingjun;
Zhang, Li;
Dai, Zong;
Cai, Chun;
Zou, Xiaoyong

Publication type:

Article

Analyzing whole genome bisulfite sequencing data from highly divergent genotypes.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. e117, doi. 10.1093/nar/gkz674

By:

Wulfridge, Phillip;
Langmead, Ben;
Feinberg, Andrew P;
Hansen, Kasper D

Publication type:

Article

Simultaneous precise editing of multiple genes in human cells.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. e116, doi. 10.1093/nar/gkz669

By:

Riesenberg, Stephan;
Chintalapati, Manjusha;
Macak, Dominik;
Kanis, Philipp;
Maricic, Tomislav;
Pääbo, Svante

Publication type:

Article

Targeted short read sequencing and assembly of re-arrangements and candidate gene loci provide megabase diplotypes.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. e115, doi. 10.1093/nar/gkz661

By:

Shin, GiWon;
Greer, Stephanie U;
Xia, Li C;
Lee, HoJoon;
Zhou, Jun;
Boles, T Christian;
Ji, Hanlee P

Publication type:

Article

Generation of a caged lentiviral vector through an unnatural amino acid for photo-switchable transduction.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. e114, doi. 10.1093/nar/gkz659

By:

Wang, Yan;
Li, Shuai;
Tian, Zhenyu;
Sun, Jiaqi;
Liang, Shuobin;
Zhang, Bo;
Bai, Lu;
Zhang, Yuanjie;
Zhou, Xueying;
Xiao, Sulong;
Zhang, Qiang;
Zhang, Lihe;
Zhang, Chuanling;
Zhou, Demin

Publication type:

Article

FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. e113, doi. 10.1093/nar/gkz658

By:

Carter, Jean-Michel;
Emmett, Warren;
Mozos, Igor Rdl;
Kotter, Annika;
Helm, Mark;
Ule, Jernej;
Hussain, Shobbir

Publication type:

Article

Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 19, p. 10134, doi. 10.1093/nar/gkz515

By:

Lountos, George T;
Zhao, Xue Zhi;
Kiselev, Evgeny;
Tropea, Joseph E;
Needle, Danielle;
Pommier, Yves;
Burke, Terrence R;
Waugh, David S

Publication type:

Article