title: Aire Downregulation Is Associated with Changes in the Posttranscriptional Control of Peripheral Tissue Antigens in Medullary Thymic Epithelial Cells.
abstract: Autoimmune regulator (Aire) is a transcriptional regulator of peripheral tissue antigens (PTAs) and microRNAs (miRNAs) in medullary thymic epithelial cells (mTECs). In this study, we tested the hypothesis that Aire also played a role as an upstream posttranscriptional controller in these cells and that variation in its expression might be associated with changes in the interactions between miRNAs and the mRNAs encoding PTAs. We demonstrated that downregulation of Airein vivoin the thymuses of BALB/c mice imbalanced the large-scale expression of these two RNA species and consequently their interactions. The expression profiles of a large set of mTEC miRNAs and mRNAs isolated from the thymuses of mice subjected (or not) to small-interfering-induced Aire gene knockdown revealed that 87 miRNAs and 4,558 mRNAs were differentially expressed. The reconstruction of the miRNA-mRNA interaction networks demonstrated that interactions between these RNAs were under Aire influence and therefore changed when this gene was downregulated. Prior to Aire-knockdown, only members of the miR-let-7 family interacted with a set of PTA mRNAs. Under Aire-knockdown conditions, a larger set of miRNA families and their members established this type of interaction. Notably, no previously described Aire-dependent PTA interacted with the miRNAs, indicating that these PTAs were somehow refractory. The miRNA-mRNA interactions were validated by calculating the minimal free energy of the pairings between the miRNA seed regions and the mRNA 3' UTRs and within the cellular milieu using the luciferase reporter gene assay. These results suggest the existence of a link between transcriptional and posttranscriptional control because Aire downregulation alters the miRNA-mRNA network controlling PTAs in mTEC cells.
authors.affiliation: Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP) , São Paulo , Brazil.
authors.forename: Ernna H
authors.initials: EH
authors.lastname: Oliveira
authors.affiliation: Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP) , São Paulo , Brazil.
authors.forename: Claudia
authors.initials: C
authors.lastname: Macedo
authors.affiliation: Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP) , São Paulo , Brazil.
authors.forename: Cristhianna V
authors.initials: CV
authors.lastname: Collares
authors.affiliation: Department of Pathology, Ribeirão Preto Medical School, University of São Paulo (USP) , São Paulo , Brazil.
authors.forename: Ana Carolina
authors.initials: AC
authors.lastname: Freitas
authors.affiliation: Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP) , São Paulo , Brazil.
authors.forename: Paula Barbim
authors.initials: PB
authors.lastname: Donate
authors.affiliation: Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo (USP) , São Paulo , Brazil.
authors.forename: Elza T
authors.initials: ET
authors.lastname: Sakamoto-Hojo
authors.affiliation: Department of Clinical Medicine, Division of Clinical Immunology, Ribeirão Preto Medical School, University of São Paulo (USP) , São Paulo , Brazil.
authors.forename: Eduardo A
authors.initials: EA
authors.lastname: Donadi
authors.affiliation: Molecular Immunogenetics Group, Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), São Paulo, Brazil; Discipline of Genetics and Molecular Biology, Department of Morphology, Physiology and Basic Pathology, School of Dentistry of Ribeirão Preto, University of São Paulo (USP), São Paulo, Brazil.
authors.forename: Geraldo A
authors.initials: GA
authors.lastname: Passos
keywords: Aire; in vivo gene knockdown; medullary thymic epithelial cells; miRNAs; miRNA–mRNA interaction; promiscuous gene expression