title: Genome-wide identification of translationally inhibited and degraded miR-155 targets using RNA-interacting protein-IP.
abstract: MicroRNAs (miRNAs) are single-stranded, small, non-coding RNAs, which fine-tune protein expression by degrading and/or translationally inhibiting mRNAs. Manipulation of miRNA expression in animal models frequently results in severe phenotypes indicating their relevance in controlling cellular functions, most likely by interacting with multiple targets. To better understand the effect of miRNA activities, genome-wide analysis of their targets are required. MicroRNA profiling as well as transcriptome analysis upon enforced miRNA expression were frequently used to investigate their relevance. However, these approaches often fail to identify relevant miRNAs targets. Therefore, we tested the precision of RNA-interacting protein immunoprecipitation (RIP) using AGO2-specific antibodies, a core component of the "RNA-induced silencing complex" (RISC), followed by RNA sequencing (Seq) in a defined cellular system, the HEK293T cells with stable, ectopic expression of miR-155. Thereby, we identified 100 AGO2-associated mRNAs in miR-155-expressing cells, of which 67 were in silico predicted miR-155 target genes. An integrated analysis of the corresponding expression profiles indicated that these targets were either regulated by mRNA decay or by translational repression. Of the identified miR-155 targets, 17 were related to cell cycle control, suggesting their involvement in the observed increase in cell proliferation of HEK293T cells upon miR-155 expression. Additional, secondary changes within the gene expression profile were detected and might contribute to this phenotype as well. Interestingly, by analyzing RIP-Seq data of HEK-293T cells and two B-cell lines we identified a recurrent disproportional enrichment of several miRNAs, including miR-155 and miRNAs of the miR-17-92 cluster, in the AGO2-associated precipitates, suggesting discrepancies in miRNA expression and activity.
authors.affiliation: German Cancer Research Center, Division of Molecular Genetics, Heidelberg, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Meier
authors.forename: Volker
authors.initials: V
authors.lastname: Hovestadt
authors.forename: Marc
authors.initials: M
authors.lastname: Zapatka
authors.forename: Armin
authors.initials: A
authors.lastname: Pscherer
authors.forename: Peter
authors.initials: P
authors.lastname: Lichter
authors.forename: Martina
authors.initials: M
authors.lastname: Seiffert
mesh_terms: D060565:Argonaute Proteins / Q000378:metabolism; D002453:Cell Cycle / Q000235:genetics / Q000502:physiology; D049109:Cell Proliferation; D002478:Cells, Cultured; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D057809:HEK293 Cells; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism*; D020871:RNA Stability; D062085:RNA, Long Noncoding; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D034743:RNA-Induced Silencing Complex / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: C466422:AGO2 protein, human; D060565:Argonaute Proteins; C568997:MIR17HG, human; C524942:MIRN155 microRNA, human; D035683:MicroRNAs; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D034743:RNA-Induced Silencing Complex
keywords: AGO2-IP; RIP-Seq; miR-155; miRNA activity; miRNA target profiling; translational inhibition