title: CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs.
abstract: Circular RNAs (circRNAs) are widely expressed in animal cells, but their biogenesis and functions are poorly understood. CircRNAs have been shown to act as sponges for miRNAs and may also potentially sponge RNA-binding proteins (RBPs) and are thus predicted to function as robust posttranscriptional regulators of gene expression. The joint analysis of large-scale transcriptome data coupled with computational analyses represents a powerful approach to elucidate possible biological roles of ribonucleoprotein (RNP) complexes. Here, we present a new web tool, CircInteractome (circRNA interactome), for mapping RBP- and miRNA-binding sites on human circRNAs. CircInteractome searches public circRNA, miRNA, and RBP databases to provide bioinformatic analyses of binding sites on circRNAs and additionally analyzes miRNA and RBP sites on junction and junction-flanking sequences. CircInteractome also allows the user the ability to (1) identify potential circRNAs which can act as RBP sponges, (2) design junction-spanning primers for specific detection of circRNAs of interest, (3) design siRNAs for circRNA silencing, and (4) identify potential internal ribosomal entry sites (IRES). In sum, the web tool CircInteractome, freely accessible at http://circinteractome.nia.nih.gov, facilitates the analysis of circRNAs and circRNP biology.
authors.affiliation: a Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health , Baltimore , Maryland 21224 , USA.
authors.forename: Dawood B
authors.initials: DB
authors.lastname: Dudekula
authors.affiliation: a Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health , Baltimore , Maryland 21224 , USA.
authors.forename: Amaresh C
authors.initials: AC
authors.lastname: Panda
authors.affiliation: a Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health , Baltimore , Maryland 21224 , USA.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Grammatikakis
authors.affiliation: a Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health , Baltimore , Maryland 21224 , USA.
authors.forename: Supriyo
authors.initials: S
authors.lastname: De
authors.affiliation: a Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health , Baltimore , Maryland 21224 , USA.
authors.forename: Kotb
authors.initials: K
authors.lastname: Abdelmohsen
authors.affiliation: a Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health , Baltimore , Maryland 21224 , USA.
authors.forename: Myriam
authors.initials: M
authors.lastname: Gorospe
mesh_terms: D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism*; D008958:Models, Molecular; D012313:RNA / Q000737:chemistry* / Q000378:metabolism*; D000079962:RNA, Circular; D016601:RNA-Binding Proteins / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D064878:Web Browser
chemical_list: D035683:MicroRNAs; D000079962:RNA, Circular; D016601:RNA-Binding Proteins; D012313:RNA
keywords: CLIP-Seq; CircRNA-miRNA; RNA-binding proteins; circRNA IRES; circRNA siRNA; divergent primer design; sponge circRNAs; transcriptome