title: Analysis of secondary structural elements in human microRNA hairpin precursors.
abstract: BACKGROUND
  MicroRNAs (miRNAs) regulate gene expression by targeting complementary mRNAs for destruction or translational repression. Aberrant expression of miRNAs has been associated with various diseases including cancer, thus making them interesting therapeutic targets. The composite of secondary structural elements that comprise miRNAs could aid the design of small molecules that modulate their function.
  
  
  RESULTS
  We analyzed the secondary structural elements, or motifs, present in all human miRNA hairpin precursors and compared them to highly expressed human RNAs with known structures and other RNAs from various organisms. Amongst human miRNAs, there are 3808 are unique motifs, many residing in processing sites. Further, we identified motifs in miRNAs that are not present in other highly expressed human RNAs, desirable targets for small molecules. MiRNA motifs were incorporated into a searchable database that is freely available. We also analyzed the most frequently occurring bulges and internal loops for each RNA class and found that the smallest loops possible prevail. However, the distribution of loops and the preferred closing base pairs were unique to each class.
  
  
  CONCLUSIONS
  Collectively, we have completed a broad survey of motifs found in human miRNA precursors, highly expressed human RNAs, and RNAs from other organisms. Interestingly, unique motifs were identified in human miRNA processing sites, binding to which could inhibit miRNA maturation and hence function.
authors.affiliation: Department of Chemistry, Scripps Florida, The Scripps Research Institute, 130 Scripps Way 3A1, Jupiter, FL, 33458, USA. biaoliu19@gmail.com.|Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA. biaoliu19@gmail.com.
authors.forename: Biao
authors.initials: B
authors.lastname: Liu
authors.affiliation: Department of Chemistry, Scripps Florida, The Scripps Research Institute, 130 Scripps Way 3A1, Jupiter, FL, 33458, USA. jdisney@scripps.edu.
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Childs-Disney
authors.affiliation: Department of Chemistry, Saint Louis University, 3501 Laclede Ave, St. Louis, MO, 63103, USA. znoskob@slu.edu.
authors.forename: Brent M
authors.initials: BM
authors.lastname: Znosko
authors.affiliation: Department of Biostatistics, Roswell Park Cancer Institute, 701 Ellicott St, Buffalo, NY, 14203, USA. Dan.Wang@Roswellpark.org.|NYS Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott St, Buffalo, NY, 14203, USA. Dan.Wang@Roswellpark.org.
authors.forename: Dan
authors.initials: D
authors.lastname: Wang
authors.affiliation: Informatics Core, The Scripps Research Institute, 130 Scripps Way 2B2, Jupiter, FL, 33458, USA. mfallahi@scripps.edu.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Fallahi
authors.affiliation: NYS Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott St, Buffalo, NY, 14203, USA. smgallo@buffalo.edu.|The State University of New York at Buffalo, Buffalo, NY, 14203, USA. smgallo@buffalo.edu.
authors.forename: Steven M
authors.initials: SM
authors.lastname: Gallo
authors.affiliation: Department of Chemistry, Scripps Florida, The Scripps Research Institute, 130 Scripps Way 3A1, Jupiter, FL, 33458, USA. Disney@scripps.edu.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Disney
mesh_terms: D005786:Gene Expression Regulation; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics*; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs / Q000235:genetics*; D012322:RNA Precursors / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors