title: Identification, validation, and characterization of noncanonical miRNAs.
abstract: Many eukaryotes and some viruses encode microRNAs (miRNAs), small RNAs that post-transcriptionally regulate gene expression. While most miRNAs are generated through the activity of RNA Polymerase II (RNAP II) and subsequent processing by Drosha and Dicer, some viral miRNAs utilize alternative pathways of biogenesis. Some members of the herpesvirus and retrovirus families can direct synthesis of miRNAs through RNAP III transcription rather than RNAP II and can utilize atypical enzymes to generate miRNAs. Though the advantages of alternative miRNA biogenesis remain unclear for herpesviruses, the retroviral miRNA biogenesis routes allow the RNAP II transcribed retroviral genome to escape Drosha cleavage while still expressing abundant, biologically-active miRNAs. These RNAP III-derived miRNAs have unique characteristics that allow for their identification and characterization. In this article, we describe procedures to predict, validate, and characterize RNAP III-transcribed miRNAs and other small RNAs, while providing resources that are also useful for canonical miRNAs.
authors.affiliation: The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Dept. Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, United States.
authors.forename: James M
authors.initials: JM
authors.lastname: Burke
authors.affiliation: The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Dept. Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, United States.
authors.forename: Chad V
authors.initials: CV
authors.lastname: Kuny
authors.affiliation: The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Dept. Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, United States.
authors.forename: Rodney P
authors.initials: RP
authors.lastname: Kincaid
authors.affiliation: The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Dept. Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, United States. Electronic address: Chris_sullivan@mail.utexas.edu.
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Sullivan
mesh_terms: D000465:Algorithms; D056890:Eukaryota / Q000378:metabolism; D006564:Herpesviridae / Q000235:genetics / Q000378:metabolism*; D035683:MicroRNAs / Q000096:biosynthesis*; D012320:RNA Polymerase III / Q000378:metabolism; D012367:RNA, Viral / Q000096:biosynthesis*; D012190:Retroviridae / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D035683:MicroRNAs; D012367:RNA, Viral; D012320:RNA Polymerase III
keywords: Dicer; Drosha; RNAP III; Virus; hsa-pri-miR-5683; miRNA; miRNA biogenesis