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01-03-2012 | Brief Report

vHoT: a database for predicting interspecies interactions between viral microRNA and host genomes

Authors: Hanjoo Kim, Seunghyun Park, Hyeyoung Min, Sungroh Yoon

Published in: Archives of Virology | Issue 3/2012

Abstract

Some viruses have been reported to transcribe microRNAs, implying complex relationships between the host and the pathogen at the post-transcriptional level through microRNAs in virus-infected cells. Although many computational algorithms have been developed for microRNA target prediction, few have been designed exclusively to find cellular or viral mRNA targets of viral microRNAs in a user-friendly manner. To address this, we introduce the viral microRNA host target (vHoT) database for predicting interspecies interactions between viral microRNA and host genomes. vHoT supports target prediction of 271 viral microRNAs from human, mouse, rat, rhesus monkey, cow, and virus genomes. vHoT is freely available at http://dna.korea.ac.kr/vhot.

Available only for authorised users

Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297PubMedCrossRef

Chen CZ, Li L, Lodish HF, Bartel DP (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science 303:83–86PubMedCrossRef

Liu C, Teng ZQ, Santistevan NJ, Szulwach KE, Guo W, Jin P, Zhao X (2010) Epigenetic regulation of mir-184 by mbd1 governs neural stem cell proliferation and differentiation. Cell Stem Cell 6:433–444PubMedCrossRef

Grey F, Tirabassi R, Meyers H, Wu G, McWeeney S, Hook L, Nelson JA (2010) A viral microRNA down-regulates multiple cell cycle genes through mRNA 5′UTRs. PLoS Pathog 6:e1000967PubMedCrossRef

Jiang S, Zhang HW, Lu MH, He XH, Li Y, Gu H, Liu MF, Wang ED (2010) MicroRNA-155 functions as an OncomiR in breast cancer by targeting the suppressor of cytokine signaling 1 gene. Cancer Res 70:3119–3127PubMedCrossRef

Grun D, Wang YL, Langenberger D, Gunsalus KC, Rajewsky N (2005) microRNA target predictions across seven drosophila species and comparison to mammalian targets. PLoS Comput Biol 1:e13PubMedCrossRef

Hsu PW, Lin LZ, Hsu SD, Hsu JB, Huang HD (2007) Vita: prediction of host microRNAs targets on viruses. Nucleic Acids Res 35:D381–D385PubMedCrossRef

Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z, Hatzigeorgiou A (2004) A combined computational-experimental approach predicts human microRNA targets. Genes Dev 18:1165–1178PubMedCrossRef

Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115:787–798PubMedCrossRef

10.

Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15–20PubMedCrossRef

11.

Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I (2006) A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell 126:1203–1217PubMedCrossRef

12.

Gottwein E, Mukherjee N, Sachse C, Frenzel C, Majoros WH, Chi JT, Braich R, Manoharan M, Soutschek J, Ohler U, Cullen BR (2007) A viral microRNA functions as an orthologue of cellular mir-155. Nature 450:1096–1099PubMedCrossRef

13.

Pfeffer S, Zavolan M, Grasser FA, Chien M, Russo JJ, Ju J, John B, Enright AJ, Marks D, Sander C, Tuschl T (2004) Identification of virus-encoded microRNAs. Science 304:734–736PubMedCrossRef

14.

Umbach JL, Kramer MF, Jurak I, Karnowski HW, Coen DM, Cullen BR (2008) MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs. Nature 454:780–783PubMed

15.

Lagana A, Forte S, Russo F, Giugno R, Pulvirenti A, Ferro A (2010) Prediction of human targets for viral-encoded microRNAs by thermodynamics and empirical constraints. J RNAi Gene Silencing 6:379–385PubMed

16.

Elefant N, Berger A, Shein H, Hofree M, Margalit H, Altuvia Y (2011) RepTar: a database of predicted cellular targets of host and viral miRNAs. Nucleic Acids Res 39:D188–D194PubMedCrossRef

17.

John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS (2004) Human microRNA targets. PLoS Biol 2:e363PubMedCrossRef

18.

Betel D, Wilson M, Gabow A, Marks DS, Sander C (2008) The microrna.org resource: targets and expression. Nucleic Acids Res 36:D149–D153PubMedCrossRef

19.

Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R (2004) Fast and effective prediction of microRNA/target duplexes. RNA 10:1507–1517PubMedCrossRef

20.

Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA, Sethupathy P, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG (2009) Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics 10:295PubMedCrossRef

21.

Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39:1278–1284PubMedCrossRef

22.

Griffiths-Jones S (2004) The microRNA registry. Nucleic Acids Res 32:D109–D111PubMedCrossRef

23.

Griffiths-Jones S (2006) miRBase: the microRNA sequence database. Methods Mol Biol 342:129–138PubMed

24.

Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: microrna sequences, targets and gene nomenclature. Nucleic Acids Res 34:D140–D144PubMedCrossRef

25.

Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154–D158PubMedCrossRef

26.

Sczyrba A, Kruger J, Mersch H, Kurtz S, Giegerich R (2003) RNA-related tools on the bielefeld bioinformatics server. Nucleic Acids Res 31:3767–3770PubMedCrossRef

27.

Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N (2008) Widespread changes in protein synthesis induced by microRNAs. Nature 455:58–63PubMedCrossRef

28.

Bessant C, Shadforth I, Oakley D (2009) Building bioinformatics solutions: with Perl, R and MySQL. Oxford biology. Oxford University Press, Oxford

29.

Descartes A, Bunce T (2000) Programming the Perl DBI. O’Reilly, Cambridge

30.

Zawodny JD, Balling DJ (2004) High performance MySQL: optimization, backups, replication, and load balancing, 1st edn. O’Reilly, Beijing

31.

Sarnow P, Jopling C, Norman K, Schutz S, Wehner K (2006) MicroRNAs: expression, avoidance and subversion by vertebrate viruses. Nat Rev Microbiol 4:651–659PubMedCrossRef

32.

Sethupathy P, Corda B, Hatzigeorgiou A (2006) Tarbase: a comprehensive database of experimentally supported animal microRNA targets. RNA 12:192–197PubMedCrossRef

33.

Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T (2009) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 37:D105–D110PubMedCrossRef

Title: vHoT: a database for predicting interspecies interactions between viral microRNA and host genomes
Authors: Hanjoo Kim
Seunghyun Park
Hyeyoung Min
Sungroh Yoon
Publication date: 01-03-2012
Publisher: Springer Vienna
Published in: Archives of Virology / Issue 3/2012
Print ISSN: 0304-8608
Electronic ISSN: 1432-8798
DOI: https://doi.org/10.1007/s00705-011-1181-y

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