Int J Med Sci 2014; 11(8):824-833. doi:10.7150/ijms.8358

Research Paper

Frequent Co-Expression of miRNA-5p and -3p Species and Cross-Targeting in Induced Pluripotent Stem Cells

Chiu-Jung Huang1✉, Phan Nguyen Nhi Nguyen2, Kong Bung Choo2,3, Shigeki Sugii4,5, Kenneth Wee4, Soon Keng Cheong2,6, Tunku Kamarul7

1. Department of Animal Science & Graduate Institute of Biotechnology, Chinese Culture University, Taipei, Taiwan;
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;
4. Singapore BioImaging Consortium, Singapore;
5. Duke-NUS Graduate Medical School, Singapore;
6. Dean's Office, Universiti Tunku Abdul Rahman, Faculty of Medicine and Health Sciences, Kajang, Selangor, Malaysia;
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.

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.

Conclusion: 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.

Keywords: Induced pluripotent stem cells, reprogramming, miRNA-5p/3p species, cell cycle control

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How to cite this article:
Huang CJ, Nguyen PNN, Choo KB, Sugii S, Wee K, Cheong SK, Kamarul T. Frequent Co-Expression of miRNA-5p and -3p Species and Cross-Targeting in Induced Pluripotent Stem Cells. Int J Med Sci 2014; 11(8):824-833. doi:10.7150/ijms.8358. Available from http://www.medsci.org/v11p0824.htm