title: Computational and experimental identification of C. elegans microRNAs.
abstract: MicroRNAs (miRNAs) constitute an extensive class of noncoding RNAs that are thought to regulate the expression of target genes via complementary base-pair interactions. To date, cloning has identified over 200 miRNAs from diverse eukaryotic organisms. Despite their success, such biochemical approaches are skewed toward identifying abundant miRNAs, unlike genome-wide, sequence-based computational predictions. We developed informatic methods to predict miRNAs in the C. elegans genome using sequence conservation and structural similarity to known miRNAs and generated 214 candidates. We confirmed the expression of four new miRNAs by Northern blotting and used a more sensitive PCR approach to verify the expression of ten additional candidates. Based on hypotheses underlying our computational methods, we estimate that the C. elegans genome may encode between 140 and 300 miRNAs and potentially many more.
authors.affiliation: The Lipper Center for Computational Genetics and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Yonatan
authors.initials: Y
authors.lastname: Grad
authors.forename: John
authors.initials: J
authors.lastname: Aach
authors.forename: Gabriel D
authors.initials: GD
authors.lastname: Hayes
authors.forename: Brenda J
authors.initials: BJ
authors.lastname: Reinhart
authors.forename: George M
authors.initials: GM
authors.lastname: Church
authors.forename: Gary
authors.initials: G
authors.lastname: Ruvkun
authors.forename: John
authors.initials: J
authors.lastname: Kim
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence / Q000235:genetics*; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism; D030541:Databases, Genetic; D019143:Evolution, Molecular; D005786:Gene Expression Regulation / Q000235:genetics*; D008492:Medical Informatics Computing; D035683:MicroRNAs / Q000032:analysis* / Q000235:genetics*; D008969:Molecular Sequence Data; D015394:Molecular Structure; D010802:Phylogeny; D015203:Reproducibility of Results; D012689:Sequence Homology, Nucleic Acid
chemical_list: D035683:MicroRNAs