title: Evidence that miRNAs are different from other RNAs.
abstract: An examination of 513 known pre-miRNAs and 237 other RNAs (tRNA, rRNA, and mRNA) revealed that miRNAs were significantly different from other RNAs (p < 0.001). miRNA genes were less conserved than other RNA genes, although their mature miRNA sequences were highly conserved. The A+U content of pre-miRNAs was higher than non-coding RNA (p < 0.001), but lower than mRNAs. The nucleotides in pre-miRNAs formed more hydrogen bonds and base pairs than in other RNAs. miRNAs had higher negative adjusted minimal folding free energies than other RNAs except tRNAs (p < 0.001). The MFE index (MFEI) was a sufficient criterion to distinguish miRNAs from all coding and non-coding RNAs (p < 0.001). The MFEI for miRNAs was 0.97, significantly higher than tRNAs (0.64), rRNAs (0.59), or mRNAs (0.65). Our findings should facilitate the prediction and identification of new miRNAs using computational and experimental strategies.
authors.affiliation: The Institute of Environmental and Human Health (TIEHH), and Department of Environmental Toxicology, Texas Tech University, Lubbock, Texas 79409-1163, USA.
authors.forename: B H
authors.initials: BH
authors.lastname: Zhang
authors.forename: X P
authors.initials: XP
authors.lastname: Pan
authors.forename: S B
authors.initials: SB
authors.lastname: Cox
authors.forename: G P
authors.initials: GP
authors.lastname: Cobb
authors.forename: T A
authors.initials: TA
authors.lastname: Anderson
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence; D018398:Homeodomain Proteins / Q000235:genetics; D035683:MicroRNAs / Q000737:chemistry*; D008969:Molecular Sequence Data; D009687:Nuclear Proteins / Q000235:genetics; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000032:analysis; D010940:Plant Proteins / Q000235:genetics; D012313:RNA / Q000737:chemistry*; D012322:RNA Precursors; D018749:RNA, Plant / Q000235:genetics*; D017385:Sequence Homology; D012689:Sequence Homology, Nucleic Acid
chemical_list: D018398:Homeodomain Proteins; D035683:MicroRNAs; D009687:Nuclear Proteins; D009711:Nucleotides; D010940:Plant Proteins; D012322:RNA Precursors; D018749:RNA, Plant; D012313:RNA