title: Frequent co-expression of miRNA-5p and -3p species and cross-targeting in induced pluripotent stem cells.
abstract: BACKGROUND
  A miRNA precursor generally gives rise to one major miRNA species derived from the 5' arm, and are called miRNA-5p. However, more recent studies have shown co-expression of miRNA-5p and -3p, albeit in different concentrations, in cancer cells targeting different sets of transcripts. Co-expression and regulation of the -5p and -3p miRNA species in stem cells, particularly in the reprogramming process, have not been studied.
  
  
  METHODS
  In this work, we investigated co-expression and regulation of miRNA-5p and -3p species in human induced pluripotent stem cells (iPSCs), mesenchymal stem cells (MSCs) and embryonic stem cells (ESC) using a nanoliter-scale real-time PCR microarray platform that included 1,036 miRNAs.
  
  
  RESULTS
  In comparing iPSC and ESC, only 32 miRNAs were found to be differentially expressed, in agreement of the ESC-like nature of iPSC. In the analysis of reprogramming process in iPSCs, 261 miRNAs were found to be differentially expressed compared with the parental MSC and pre-adipose tissue, indicating significant miRNA alternations in the reprogramming process. In iPSC reprogrammed from MSC, there were 88 miRNAs (33.7%), or 44 co-expressed 5p/3p pairs, clearly indicating frequent co-expression of both miRNA species on reprogramming. Of these, 40 pairs were either co-up- or co-downregulated indicating concerted 5p/3p regulation. The 5p/3p species of only 4 pairs were regulated in reverse directions. Furthermore, some 5p/3p species of the same miRNAs were found to target the same transcript and the same miRNA may cross-target different transcripts of proteins of the G1/S transition of the cell cycle; 5p/3p co-targeting was confirmed in stem-loop RT-PCR.
  
  
  CONCLUSIONS
  The observed cross- and co-regulation by paired miRNA species suggests a fail-proof scheme of miRNA regulation in iPSC, which may be important to iPSC pluripotency.
authors.affiliation: 1. Department of Animal Science & Graduate Institute of Biotechnology, Chinese Culture University, Taipei, Taiwan;
authors.forename: Chiu-Jung
authors.initials: CJ
authors.lastname: Huang
authors.affiliation: 2. Centre for Stem Cell Research, Universiti Tunku Abdul Rahman, Faculty of Medicine and Health Sciences, Kajang, Selangor, Malaysia;
authors.forename: Phan Nguyen Nhi
authors.initials: PN
authors.lastname: Nguyen
authors.affiliation: 2. Centre for Stem Cell Research, Universiti Tunku Abdul Rahman, Faculty of Medicine and Health Sciences, Kajang, Selangor, Malaysia; ; 3. Department of Preclinical Sciences, Universiti Tunku Abdul Rahman, Faculty of Medicine and Health Sciences, Kajang, Selangor, Malaysia;
authors.forename: Kong Bung
authors.initials: KB
authors.lastname: Choo
authors.affiliation: 4. Singapore BioImaging Consortium, Singapore; ; 5. Duke-NUS Graduate Medical School, Singapore;
authors.forename: Shigeki
authors.initials: S
authors.lastname: Sugii
authors.affiliation: 4. Singapore BioImaging Consortium, Singapore;
authors.forename: Kenneth
authors.initials: K
authors.lastname: Wee
authors.affiliation: 2. Centre for Stem Cell Research, Universiti Tunku Abdul Rahman, Faculty of Medicine and Health Sciences, Kajang, Selangor, Malaysia; ; 6. Dean's Office, Universiti Tunku Abdul Rahman, Faculty of Medicine and Health Sciences, Kajang, Selangor, Malaysia;
authors.forename: Soon Keng
authors.initials: SK
authors.lastname: Cheong
authors.affiliation: 7. Tissue Engineering Group, National Orthopaedic Centre of Excellence for Research and Learning, Department of Orthopaedic Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Tunku
authors.initials: T
authors.lastname: Kamarul
mesh_terms: D002454:Cell Differentiation; D065150:Cellular Reprogramming / Q000235:genetics; D053595:Embryonic Stem Cells / Q000378:metabolism*; D018507:Gene Expression Regulation, Developmental; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000378:metabolism*; D059630:Mesenchymal Stem Cells / Q000378:metabolism*; D035683:MicroRNAs / Q000096:biosynthesis* / Q000235:genetics
chemical_list: D035683:MicroRNAs
keywords: Induced pluripotent stem cells; cell cycle control; miRNA-5p/3p species; reprogramming