Works matching IS 03051048 AND DT 2015 AND VI 43 AND IP 3

Results: 64

Recombinase and translesion DNA polymerase decrease the speed of replication fork progression during the DNA damage response in Escherichia coli cells.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1714, doi. 10.1093/nar/gkv044

By:

Tan, Kang Wei;
Pham, Tuan Minh;
Furukohri, Asako;
Maki, Hisaji;
Akiyama, Masahiro Tatsumi

Publication type:

Article

Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1859, doi. 10.1093/nar/gkv010

By:

Corley, Meredith;
Solem, Amanda;
Qu, Kun;
Chang, Howard Y.;
Laederach, Alain

Publication type:

Article

DNA lesion identity drives choice of damage tolerance pathway in murine cell chromosomes.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1637, doi. 10.1093/nar/gku1398

By:

Cohen, Isadora S.;
Bar, Carmit;
Paz-Elizur, Tamar;
Ainbinder, Elena;
Leopold, Karoline;
de Wind, Niels;
Geacintov, Nicholas;
Livneh, Zvi

Publication type:

Article

The solution structure of the pentatricopeptide repeat protein PPR10 upon binding atpH RNA.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1918, doi. 10.1093/nar/gkv027

By:

Gully, Benjamin S.;
Cowieson, Nathan;
Stanley, Will A.;
Shearston, Kate;
Small, Ian D.;
Barkan, Alice;
Bond, Charles S.

Publication type:

Article

Identification of the target DNA sequence and characterization of DNA binding features of HlyU, and suggestion of a redox switch for hlyA expression in the human pathogen Vibrio cholerae from in silico studies.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1407, doi. 10.1093/nar/gku1319

By:

Mukherjee, Debadrita;
Pal, Aritrika;
Chakravarty, Devlina;
Chakrabarti, Pinak

Publication type:

Article

GRASP: Guided Reference-based Assembly of Short Peptides.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. e18, doi. 10.1093/nar/gku1210

By:

Zhong, Cuncong;
Yang, Youngik;
Yooseph, Shibu

Publication type:

Article

DICER-dependent biogenesis of let-7 miRNAs affects human cell response to DNA damage via targeting p21/p27.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1626, doi. 10.1093/nar/gku1368

By:

Liu, Bailong;
Liu, Min;
Wang, Jian;
Zhang, Xiangming;
Wang, Xiang;
Wang, Ping;
Wang, Hongyan;
Li, Wei;
Wang, Ya

Publication type:

Article

Identification of protein complexes that bind to histone H3 combinatorial modifications using super-SILAC and weighted correlation network analysis.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1418, doi. 10.1093/nar/gku1350

By:

Kunowska, Natalia;
Rotival, Maxime;
Yu, Lu;
Choudhary, Jyoti;
Dillon, Niall

Publication type:

Article

The principal mRNA nuclear export factor NXF1:NXT1 forms a symmetric binding platform that facilitates export of retroviral CTE-RNA.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1883, doi. 10.1093/nar/gkv032

By:

Aibara, Shintaro;
Katahira, Jun;
Valkov, Eugene;
Stewart, Murray

Publication type:

Article

ZBTB2 increases PDK4 expression by transcriptional repression of RelA/p65.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1609, doi. 10.1093/nar/gkv026

By:

Kim, Min-Young;
Koh, Dong-In;
Choi, Won-Il;
Jeon, Bu-Nam;
Jeong, Deok-yoon;
Kim, Kyung-Sup;
Kim, Kunhong;
Kim, Se-Hoon;
Hur, Man-Wook

Publication type:

Article

A KALA-modified lipid nanoparticle containing CpG-free plasmid DNA as a potential DNA vaccine carrier for antigen presentation and as an immune-stimulative adjuvant.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1317, doi. 10.1093/nar/gkv008

By:

Miura, Naoya;
Shaheen, Sharif M.;
Akita, Hidetaka;
Nakamura, Takashi;
Harashima, Hideyoshi

Publication type:

Article

A moonlighting metabolic protein influences repair at DNA double-stranded breaks.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1646, doi. 10.1093/nar/gku1405

By:

Torres-Machorro, Ana Lilia;
Aris, John P.;
Pillus, Lorraine

Publication type:

Article

A basal level of DNA damage and telomere deprotection increases the sensitivity of cancer cells to G-quadruplex interactive compounds.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1759, doi. 10.1093/nar/gkv006

By:

Salvati, Erica;
Rizzo, Angela;
Iachettini, Sara;
Zizza, Pasquale;
Cingolani, Chiara;
D'Angelo, Carmen;
Porru, Manuela;
Mondello, Chiara;
Aiello, Aurora;
Farsetti, Antonella;
Gilson, Eric;
Leonetti, Carlo;
Biroccio, Annamaria

Publication type:

Article

A defense-offense multi-layered regulatory switch in a pathogenic bacterium.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1357, doi. 10.1093/nar/gkv001

By:

Nitzan, Mor;
Fechter, Pierre;
Peer, Asaf;
Altuvia, Yael;
Bronesky, Delphine;
Vandenesch, François;
Romby, Pascale;
Biham, Ofer;
Margalit, Hanah

Publication type:

Article

The ATP-mediated formation of the YgjD–YeaZ–YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1804, doi. 10.1093/nar/gku1397

By:

Zhang, Wenhua;
Collinet, Bruno;
Perrochia, Ludovic;
Durand, Dominique;
van Tilbeurgh, Herman

Publication type:

Article

53BP1 promotes microhomology-mediated end-joining in G1-phase cells.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1659, doi. 10.1093/nar/gku1406

By:

Xiong, Xiahui;
Du, Zhanwen;
Wang, Ying;
Feng, Zhihui;
Fan, Pan;
Yan, Chunhong;
Willers, Henning;
Zhang, Junran

Publication type:

Article

Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. e17, doi. 10.1093/nar/gku1198

By:

Ho, Tsui-Ting;
Zhou, Nanjiang;
Huang, Jianguo;
Koirala, Pratirodh;
Xu, Min;
Fung, Roland;
Wu, Fangting;
Mo, Yin-Yuan

Publication type:

Article

Sparse expression bases in cancer reveal tumor drivers.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1332, doi. 10.1093/nar/gku1290

By:

Logsdon, Benjamin A.;
Gentles, Andrew J.;
Miller, Chris P.;
Blau, C. Anthony;
Becker, Pamela S.;
Lee, Su-In

Publication type:

Article

A minimal ubiquitous chromatin opening element (UCOE) effectively prevents silencing of juxtaposed heterologous promoters by epigenetic remodeling in multipotent and pluripotent stem cells.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1577, doi. 10.1093/nar/gkv019

By:

Müller-Kuller, Uta;
Ackermann, Mania;
Kolodziej, Stephan;
Brendel, Christian;
Fritsch, Jessica;
Lachmann, Nico;
Kunkel, Hana;
Lausen, Jörn;
Schambach, Axel;
Moritz, Thomas;
Grez, Manuel

Publication type:

Article

Interaction between the RNA-dependent ATPase and poly(A) polymerase subunits of the TRAMP complex is mediated by short peptides and important for snoRNA processing.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1848, doi. 10.1093/nar/gkv005

By:

Losh, Jillian S.;
King, Alejandra Klauer;
Bakelar, Jeremy;
Taylor, Lacy;
Loomis, John;
Rosenzweig, Jason A.;
Johnson, Sean J.;
van Hoof, Ambro

Publication type:

Article

Repressor activity of the RpoS/σS-dependent RNA polymerase requires DNA binding.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1456, doi. 10.1093/nar/gku1379

By:

Lévi-Meyrueis, Corinne;
Monteil, Véronique;
Sismeiro, Odile;
Dillies, Marie-Agnès;
Kolb, Annie;
Monot, Marc;
Dupuy, Bruno;
Duarte, Sara Serradas;
Jagla, Bernd;
Coppée, Jean-Yves;
Beraud, Mélanie;
Norel, Françoise

Publication type:

Article

ModuleBlast: identifying activated sub-networks within and across species.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. e20, doi. 10.1093/nar/gku1224

By:

Zinman, Guy E.;
Naiman, Shoshana;
O'Dee, Dawn M.;
Kumar, Nishant;
Nau, Gerard J.;
Cohen, Haim Y.;
Bar-Joseph, Ziv

Publication type:

Article

Evaluating the potential for undesired genomic effects of the piggyBac transposon system in human cells.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1770, doi. 10.1093/nar/gkv017

By:

Saha, Sunandan;
Woodard, Lauren E.;
Charron, Elizabeth M.;
Welch, Richard C.;
Rooney, Cliona M.;
Wilson, Matthew H.

Publication type:

Article

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. e15, doi. 10.1093/nar/gku1196

By:

Croucher, Nicholas J.;
Page, Andrew J.;
Connor, Thomas R.;
Delaney, Aidan J.;
Keane, Jacqueline A.;
Bentley, Stephen D.;
Parkhill, Julian;
Harris, Simon R.

Publication type:

Article

Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1749, doi. 10.1093/nar/gku1407

By:

Wei, Yunzhou;
Chesne, Megan T.;
Terns, Rebecca M.;
Terns, Michael P.

Publication type:

Article

Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1345

By:

Sebestyén, Endre;
Zawisza, Michał;
Eyras, Eduardo

Publication type:

Article

Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. e21, doi. 10.1093/nar/gku1246

By:

Byrne, Susan M.;
Ortiz, Luis;
Mali, Prashant;
Aach, John;
Church, George M.

Publication type:

Article

A systematic survey of the Cys2His2 zinc finger DNA-binding landscape.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1965, doi. 10.1093/nar/gku1395

By:

Persikov, Anton V.;
Wetzel, Joshua L.;
Rowland, Elizabeth F.;
Oakes, Benjamin L.;
Xu, Denise J.;
Singh, Mona;
Noyes, Marcus B.

Publication type:

Article

Protein mistranslation protects bacteria against oxidative stress.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1740, doi. 10.1093/nar/gku1404

By:

Fan, Yongqiang;
Wu, Jiang;
Ung, Matthew H.;
De Lay, Nicholas;
Cheng, Chao;
Ling, Jiqiang

Publication type:

Article

Amplification of small molecule-inducible gene expression via tuning of intracellular receptor densities.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1955, doi. 10.1093/nar/gku1388

By:

Wang, Baojun;
Barahona, Mauricio;
Buck, Martin

Publication type:

Article

Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1905, doi. 10.1093/nar/gkv021

By:

Richet, Nicolas;
Liu, Danni;
Legrand, Pierre;
Velours, Christophe;
Corpet, Armelle;
Gaubert, Albane;
Bakail, May;
Moal-Raisin, Gwenaelle;
Guerois, Raphael;
Compper, Christel;
Besle, Arthur;
Guichard, Berengère;
Almouzni, Genevieve;
Ochsenbein, Françoise

Publication type:

Article

Primary and secondary siRNA synthesis triggered by RNAs from food bacteria in the ciliate Paramecium tetraurelia.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1818, doi. 10.1093/nar/gku1331

By:

Carradec, Quentin;
Götz, Ulrike;
Arnaiz, Olivier;
Pouch, Juliette;
Simon, Martin;
Meyer, Eric;
Marker, Simone

Publication type:

Article

Functional regulation of the DNA damage-recognition factor DDB2 by ubiquitination and interaction with xeroderma pigmentosum group C protein.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1700, doi. 10.1093/nar/gkv038

By:

Matsumoto, Syota;
Fischer, Eric S.;
Yasuda, Takeshi;
Dohmae, Naoshi;
Iwai, Shigenori;
Mori, Toshio;
Nishi, Ryotaro;
Yoshino, Ken-ichi;
Sakai, Wataru;
Hanaoka, Fumio;
Thomä, Nicolas H.;
Sugasawa, Kaoru

Publication type:

Article

The ATP binding site of the chromatin remodeling homolog Lsh is required for nucleosome density and de novo DNA methylation at repeat sequences.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1444, doi. 10.1093/nar/gku1371

By:

Ren, Jianke;
Briones, Victorino;
Barbour, Samantha;
Yu, Weishi;
Han, Yixing;
Terashima, Minoru;
Muegge, Kathrin

Publication type:

Article

Alternative splicing regulates the expression of G9A and SUV39H2 methyltransferases, and dramatically changes SUV39H2 functions.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1869, doi. 10.1093/nar/gkv013

By:

Mauger, Oriane;
Klinck, Roscoe;
Chabot, Benoit;
Muchardt, Christian;
Allemand, Eric;
Batsché, Eric

Publication type:

Article

BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. e19, doi. 10.1093/nar/gku1211

By:

Abo, Ryan P.;
Ducar, Matthew;
Garcia, Elizabeth P.;
Thorner, Aaron R.;
Rojas-Rudilla, Vanesa;
Lin, Ling;
Sholl, Lynette M.;
Hahn, William C.;
Meyerson, Matthew;
Lindeman, Neal I.;
Van Hummelen, Paul;
MacConaill, Laura E.

Publication type:

Article

The Krüppel-associated box repressor domain induces reversible and irreversible regulation of endogenous mouse genes by mediating different chromatin states.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1549, doi. 10.1093/nar/gkv016

By:

Ying, Yue;
Yang, Xingyu;
Zhao, Kai;
Mao, Jifang;
Kuang, Ying;
Wang, Zhugang;
Sun, Ruilin;
Fei, Jian

Publication type:

Article

Opposing roles of H3- and H4-acetylation in the regulation of nucleosome structure—a FRET study.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1433, doi. 10.1093/nar/gku1354

By:

Gansen, Alexander;
Tóth, Katalin;
Schwarz, Nathalie;
Langowski, Jörg

Publication type:

Article

Enhancer modeling uncovers transcriptional signatures of individual cardiac cell states in Drosophila.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1726, doi. 10.1093/nar/gkv011

By:

Busser, Brian W.;
Haimovich, Julian;
Huang, Di;
Ovcharenko, Ivan;
Michelson, Alan M.

Publication type:

Article

DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1513, doi. 10.1093/nar/gku1390

By:

Narasimhan, Kamesh;
Pillay, Shubhadra;
Huang, Yong-Heng;
Jayabal, Sriram;
Udayasuryan, Barath;
Veerapandian, Veeramohan;
Kolatkar, Prasanna;
Cojocaru, Vlad;
Pervushin, Konstantin;
Jauch, Ralf

Publication type:

Article

Human regulator of telomere elongation helicase 1 (RTEL1) is required for the nuclear and cytoplasmic trafficking of pre-U2 RNA.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1834, doi. 10.1093/nar/gku1402

By:

Schertzer, Michael;
Jouravleva, Karina;
Perderiset, Mylene;
Dingli, Florent;
Loew, Damarys;
Le Guen, Tangui;
Bardoni, Barbara;
de Villartay, Jean-Pierre;
Revy, Patrick;
Londoño-Vallejo, Arturo

Publication type:

Article

Two novel NAC transcription factors regulate gene expression and flowering time by associating with the histone demethylase JMJ14.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1469, doi. 10.1093/nar/gku1382

By:

Ning, Yong-Qiang;
Ma, Ze-Yang;
Huang, Huan-Wei;
Mo, Huixian;
Zhao, Ting-ting;
Li, Lin;
Cai, Tao;
Chen, She;
Ma, Ligeng;
He, Xin-Jian

Publication type:

Article

Nucleic Acids Research: Editorial Board.

Published in:: Nucleic Acids Research, 2015, v. 43, n. 3, p. ii, doi. 10.1093/nar/gkv130
Publication type:: Article

Defining the transcriptomic landscape of Candida glabrata by RNA-Seq.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1392, doi. 10.1093/nar/gku1357

By:

Linde, Jörg;
Duggan, Seána;
Weber, Michael;
Horn, Fabian;
Sieber, Patricia;
Hellwig, Daniela;
Riege, Konstantin;
Marz, Manja;
Martin, Ronny;
Guthke, Reinhard;
Kurzai, Oliver

Publication type:

Article

Subscriptions.

Published in:: Nucleic Acids Research, 2015, v. 43, n. 3, p. iii, doi. 10.1093/nar/gkv131
Publication type:: Article

A physiological significance of the functional interaction between Mus81 and Rad27 in homologous recombination repair.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1684, doi. 10.1093/nar/gkv025

By:

Thu, Huong Phung Thi;
Nguyen, Tuan Anh;
Munashingha, Palinda Ruvan;
Kwon, Buki;
Dao Van, Quy;
Seo, Yeon-Soo

Publication type:

Article

Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1380, doi. 10.1093/nar/gkv050

By:

Gumienny, Rafal;
Zavolan, Mihaela

Publication type:

Article

RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1370, doi. 10.1093/nar/gkv020

By:

Suresh, V.;
Liu, Liang;
Adjeroh, Donald;
Zhou, Xiaobo

Publication type:

Article

Function of the N-terminal segment of the RecA-dependent nuclease Ref.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1795, doi. 10.1093/nar/gku1330

By:

Gruber, Angela J.;
Olsen, Tayla M.;
Dvorak, Rachel H.;
Cox, Michael M.

Publication type:

Article

Multilayered genetic safeguards limit growth of microorganisms to defined environments.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. 1945, doi. 10.1093/nar/gku1378

By:

Gallagher, Ryan R.;
Patel, Jaymin R.;
Interiano, Alexander L.;
Rovner, Alexis J.;
Isaacs, Farren J.

Publication type:

Article