title: Discrimination of the expression of paralogous microRNA precursors that share the same major mature form.
abstract: BACKGROUND
  MicroRNAs (miRNAs) are a class of small non-coding RNAs generated from endogenous transcripts that form hairpin structures. The hairpin precursor is processed into two mature miRNAs that form major/minor duplexes. Mature miRNAs regulate gene expression by cleaving mRNA or repressing protein translation. Numerous miRNAs have been discovered via deep sequencing. Many miRNAs are produced from multiple genome sites. These miRNAs are grouped into paralogous families of miRNAs that generate the same major mature form within organisms. Currently, no method of distinguishing the expression of these miRNAs is available.
  
  
  RESULTS
  In the present study, strategies were developed to discriminate and quantify the expression of paralogous miRNA precursors. First, paralogous miRNA precursors that were differentially expressed in tissues were identified through analysis of the coexpression scores of their major and minor forms based on deep sequencing data. Then the precursors were identified by monitoring the expression of their host gene or minor form using real-time PCR. Finally, precursors were identified by assessing the expression of clusters of miRNA members. These approaches were used to distinguish miR-128-1 and miR-128-2 as well as miR-194-1 and miR-194-2. The mechanism of transcription related to the differential expression of miR-194-1 and miR-194-2 was also investigated.
  
  
  CONCLUSIONS
  This is the first report to distinguish paralogous miRNA copies by analyzing the expression of major-minor pairs, the host gene, and miRNA clusters. Discriminating paralogous precursors can provide useful information for investigating the mechanisms that regulate miRNA gene expression under different physiological and pathological conditions.
authors.affiliation: Department of Biochemical and Molecular Biology, Medical College, Soochow University, Suzhou, Jiangsu, China.
authors.forename: Minghua
authors.initials: M
authors.lastname: Wang
authors.affiliation: Department of Biochemical and Molecular Biology, Medical College, Soochow University, Suzhou, Jiangsu, China.
authors.forename: Weiping
authors.initials: W
authors.lastname: Wang
authors.affiliation: Department of Biochemical and Molecular Biology, Medical College, Soochow University, Suzhou, Jiangsu, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Department of Biochemical and Molecular Biology, Medical College, Soochow University, Suzhou, Jiangsu, China.
authors.forename: Juanjuan
authors.initials: J
authors.lastname: Xiao
authors.affiliation: Department of Biochemical and Molecular Biology, Medical College, Soochow University, Suzhou, Jiangsu, China.
authors.forename: Jianguo
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Physiological Sciences, Oklahoma State University, Stillwater, Oklahoma, United States of America.
authors.forename: Chaoqun
authors.initials: C
authors.lastname: Huang
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D020869:Gene Expression Profiling; D051379:Mice; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000235:genetics / Q000378:metabolism*; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors