title: Systematic analysis of viral and cellular microRNA targets in cells latently infected with human gamma-herpesviruses by RISC immunoprecipitation assay.
abstract: The mRNA targets of microRNAs (miRNAs) can be identified by immunoprecipitation of Argonaute (Ago) protein-containing RNA-induced silencing complexes (RISCs) followed by microarray analysis (RIP-Chip). Here we used Ago2-based RIP-Chip to identify transcripts targeted by Kaposi's sarcoma-associated herpesvirus (KSHV) miRNAs (n = 114), Epstein-Barr virus (EBV) miRNAs (n = 44), and cellular miRNAs (n = 2337) in six latently infected or stably transduced human B cell lines. Of the six KSHV miRNA targets chosen for validation, four showed regulation via their 3'UTR, while two showed regulation via binding sites within coding sequences. Two genes governing cellular transport processes (TOMM22 and IPO7) were confirmed to be targeted by EBV miRNAs. A significant number of viral miRNA targets were upregulated in infected cells, suggesting that viral miRNAs preferentially target cellular genes induced upon infection. Transcript half-life both of cellular and viral miRNA targets negatively correlated with recruitment to RISC complexes, indicating that RIP-Chip offers a quantitative estimate of miRNA function.
authors.affiliation: Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany.
authors.forename: Lars
authors.initials: L
authors.lastname: Dölken
authors.affiliation: Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany.
authors.forename: Georg
authors.initials: G
authors.lastname: Malterer
authors.affiliation: Institute for Informatics, Ludwig-Maximilians-University Munich, Amalienstrasse 17, 80333 Munich, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Erhard
authors.affiliation: Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany.
authors.forename: Sheila
authors.initials: S
authors.lastname: Kothe
authors.affiliation: Institute for Informatics, Ludwig-Maximilians-University Munich, Amalienstrasse 17, 80333 Munich, Germany.
authors.forename: Caroline C
authors.initials: CC
authors.lastname: Friedel
authors.affiliation: Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, Université de Strasbourg, 67084 Strasbourg, France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Suffert
authors.affiliation: Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany.
authors.forename: Lisa
authors.initials: L
authors.lastname: Marcinowski
authors.affiliation: Institute of Virology, Haus 47, Universitätsklinikum des Saarlandes, 66421 Homburg/Saar, Germany.
authors.forename: Natalie
authors.initials: N
authors.lastname: Motsch
authors.affiliation: Institute of Virology, Haus 47, Universitätsklinikum des Saarlandes, 66421 Homburg/Saar, Germany.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Barth
authors.affiliation: Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
authors.forename: Michaela
authors.initials: M
authors.lastname: Beitzinger
authors.affiliation: Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany.
authors.forename: Diana
authors.initials: D
authors.lastname: Lieber
authors.affiliation: Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany.
authors.forename: Susanne M
authors.initials: SM
authors.lastname: Bailer
authors.affiliation: Institute of Medical Microbiology, Technical University Munich, Trogerstrasse 30, 81675 Munich, Germany.
authors.forename: Reinhard
authors.initials: R
authors.lastname: Hoffmann
authors.affiliation: Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany.
authors.forename: Zsolt
authors.initials: Z
authors.lastname: Ruzsics
authors.affiliation: Helmholtz Zentrum München, Institut für Molekulare Immunologie, Marchioninistraße 25, 81377 Munich, Germany.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Kremmer
authors.affiliation: Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, Université de Strasbourg, 67084 Strasbourg, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Pfeffer
authors.affiliation: Institute for Informatics, Ludwig-Maximilians-University Munich, Amalienstrasse 17, 80333 Munich, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Zimmer
authors.affiliation: Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany.
authors.forename: Ulrich H
authors.initials: UH
authors.lastname: Koszinowski
authors.affiliation: Institute of Virology, Haus 47, Universitätsklinikum des Saarlandes, 66421 Homburg/Saar, Germany.
authors.forename: Friedrich
authors.initials: F
authors.lastname: Grässer
authors.affiliation: Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
authors.forename: Gunter
authors.initials: G
authors.lastname: Meister
authors.affiliation: Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany; Division of Pathway Medicine, University of Edinburgh, 49 Little France Crescent, Edinburgh EH16 4SB, UK. Electronic address: haas@lmb.uni-muenchen.de.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Haas
mesh_terms: D002460:Cell Line; D002478:Cells, Cultured; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D005786:Gene Expression Regulation; D015967:Gene Expression Regulation, Viral; D004854:Herpesvirus 4, Human / Q000235:genetics*; D019288:Herpesvirus 8, Human / Q000235:genetics*; D054884:Host-Pathogen Interactions; D006801:Humans; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D046228:Microarray Analysis; D012367:RNA, Viral / Q000378:metabolism; D014773:Virology / Q000379:methods*
chemical_list: D035683:MicroRNAs; D012367:RNA, Viral