Frequent co-expression of miRNA-5p and -3p species and cross-targeting in induced pluripotent stem cells

International Journal of Medical Sciences

Volumn 11, Issue 8, 2014, Pages 824-833

  Huang, Chiu Jung ^a   Nhi Nguyen, Phan Nguyen ^b   Choo, Kong Bung ^b   Sugii, Shigeki ^c,d   Wee, Kenneth ^c   Cheong, Soon Keng ^b   Kamarul, Tunku ^e  

^a CHINESE CULTURE UNIVERSITY   (Taiwan)

^b UNIVERSITI TUNKU ABDUL RAHMAN   (Malaysia)

^c AGENCY FOR SCIENCE   (Singapore)

^d DUKE NUS MEDICAL SCHOOL   (Singapore)

^e UNIVERSITY OF MALAYA   (Malaysia)

Author keywords

Cell cycle control; Induced pluripotent stem cells; miRNA 5p 3p species; Reprogramming

Indexed keywords

MICRORNA; MICRORNA 3P; MICRORNA 5P; TRANSFORMING GROWTH FACTOR BETA; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; ADIPOSE TISSUE; ARTICLE; CELL CYCLE PHASE; CONTROLLED STUDY; DOWN REGULATION; EMBRYONIC STEM CELL; G1 PHASE CELL CYCLE CHECKPOINT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; MESENCHYMAL STEM CELL; MICROARRAY ANALYSIS; NUCLEAR REPROGRAMMING; PLURIPOTENT STEM CELL; PROTEIN EXPRESSION; PROTEIN TARGETING; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; UPREGULATION; BIOSYNTHESIS; CELL DIFFERENTIATION; GENETICS; MESENCHYMAL STROMA CELL; METABOLISM;

CELL DIFFERENTIATION; CELLULAR REPROGRAMMING; EMBRYONIC STEM CELLS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HUMANS; INDUCED PLURIPOTENT STEM CELLS; MESENCHYMAL STROMAL CELLS; MICRORNAS;

EID: 84902078438     PISSN: 14491907     EISSN: None     Source Type: Journal    
DOI: 10.7150/ijms.8358     Document Type: Article

References (54)

1. Bradley A, Evans M, Kaufman MH, Robertson E. Formation of germ-line chimaeras from embryo-derived teratocarcinoma cell lines. Nature. 1984; 309(5965): 255-6.
2. Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006; 126(4): 663-76.
3. Houbaviy HB, Murray MF, Sharp PA. Embryonic stem cell-specific MicroRNAs. Dev Cell. 2003; 5(2): 351-8.
4. Wang Y, Baskerville S, Shenoy A, Babiarz JE, Baehner L, Blelloch R. Embryonic stem cell-specific microRNAs regulate the G1-S transition and promote rapid proliferation. Nat Genet. 2008; 40(12): 1478-83.
5. Wang Y, Melton C, Li YP, et al. miR-294/miR-302 promotes proliferation, suppresses G1-S restriction point, and inhibits ESC differentiation through separable mechanisms. Cell reports. 2013; 4(1): 99-109.
6. Lin SL, Chang DC, Chang-Lin S, et al. Mir-302 reprograms human skin cancer cells into a pluripotent ES-cell-like state. RNA. 2008; 14(10): 2115-24.
7. Anokye-Danso F, Trivedi CM, Juhr D, et al. Highly efficient miRNA-mediated reprogramming of mouse and human somatic cells to pluripotency. Cell Stem Cell. 2011; 8(4): 376-88.
8. Liao B, Bao X, Liu L, et al. MicroRNA cluster 302-367 enhances somatic cell reprogramming by accelerating a mesenchymal-to-epithelial transition. J Biol Chem. 2011; 286(19): 17359-64.
9. Bushati N, Cohen SM. microRNA functions. Annu Rev Cell Dev Biol. 2007; 23: 175-205.
10. Lee Y, Jeon K, Lee JT, Kim S, Kim VN. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 2002; 21(17): 4663-70.
11. O'Toole AS, Miller S, Haines N, Zink MC, Serra MJ. Comprehensive thermodynamic analysis of 3' double-nucleotide overhangs neighboring Watson-Crick terminal base pairs. Nucleic Acids Res. 2006;34(11): 3338-44.
12. Ro S, Park C, Young D, Sanders KM, Yan W. Tissue-dependent paired expression of miRNAs. Nucleic Acids Res. 2007; 35(17): 5944-53.
13. Okamura K, Phillips MD, Tyler DM, Duan H, Chou YT, Lai EC. The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution. Nat Struct Mol Biol. 2008; 15(4): 354-63.
14. Jagadeeswaran G, Zheng Y, Sumathipala N, et al. Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development. BMC genomics. 2010; 11:52.
15. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 2006; 34(Database issue): D140-4.
16. Almeida MI, Nicoloso MS, Zeng L, et al. Strand-specific miR-28-5p and miR-28-3p have distinct effects in colorectal cancer cells. Gastroenterology. 2012; 142(4): 886-96 e9.
17. Jazdzewski K, Liyanarachchi S, Swierniak M, et al. Polymorphic mature microRNAs from passenger strand of pre-miR-146a contribute to thyroid cancer. Proc Natl Acad Sci USA. 2009; 106(5): 1502-5.
18. Jiang L, Huang Q, Zhang S, et al. Hsa-miR-125a-3p and hsa-miR-125a-5p are downregulated in non-small cell lung cancer and have inverse effects on invasion and migration of lung cancer cells. BMC cancer. 2010; 10: 318.
19. Martin EC, Elliott S, Rhodes LV, et al. Preferential star strand biogenesis of pre-miR-24-2 targets PKC-alpha and suppresses cell survival in MCF-7 breast cancer cells. Mol Carcinog. 2012; [Epub ahead of print]
20. Shan SW, Fang L, Shatseva T, et al. Mature miR-17-5p and passenger miR-17-3p induce hepatocellular carcinoma by targeting PTEN, GalNT7 and vimentin in different signal pathways. J Cell Sci. 2013; 126(Pt 6): 1517-30.
21. Koh W, Sheng CT, Tan B, et al. Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of hepatic nuclear factor 4 alpha. BMC genomics. 2010; 11 Suppl 1: S6.
22. Huang X, Gschweng E, Van Handel B, Cheng D, Mikkola HK, Witte ON. Regulated expression of microRNAs-126/126* inhibits erythropoiesis from human embryonic stem cells. Blood. 2011; 117(7): 2157-65.
23. Sugii S, Kida Y, Kawamura T, et al. Human and mouse adipose-derived cells support feeder independent induction of pluripotent stem cells. Proc Natl Acad Sci USA. 2010; 107(8): 3558-63.
24. Sugii S, Kida Y, Berggren WT, Evans RM. Feeder-dependent and feeder-independent iPS cell derivation from human and mouse adipose stem cells. Nat Protoc. 2011; 6(3): 346-58.
25. Pritchard CC, Cheng HH, Tewari M. MicroRNA profiling: approaches and considerations. Nat Rev Genet. 2012; 13(5): 358-69.
26. Mestdagh P, van Vlierberghe P, de Weer A, Muth D, Westermann F, Speleman F, Vandesompele J. A novel and universal method for microRNA RT-qPCR data normalization. Genome Biol. 2009; 10(6):R64
27. Chen C, Ridzon D A, Broomer A J, et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 2005; 33(20):e179.
28. Paraskevopoulou MD, Georgakilas G, Kostoulas N, et al. DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows. Nucleic Acids Res. 2013; 41(Web Server issue): W169-73.
29. Ong WK, Sugii S. Adipose-derived stem cells: fatty potentials for therapy. Int J Biochem Cell Biol. 2013; 45(6):1083-6.
30. Sachdeva M, Zhu S, Wu F, et al. p53 represses c-Myc through induction of the tumor suppressor miR-145. Proc Natl Acad Sci USA. 2009; 106(9): 3207-12.
31. Xu N, Papagiannakopoulos T, Pan G, Thomson JA, Kosik KS. MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells. Cell. 2009; 137(4): 647-58.
32. Zhong X, Li N, Liang S, Huang Q, Coukos G, Zhang L. Identification of microRNAs regulating reprogramming factor LIN28 in embryonic stem cells and cancer cells. J Biol Chem. 2010; 285(53): 41961-71.
33. Tay YM, Tam WL, Ang YS, et al. MicroRNA-134 modulates the differentiation of mouse embryonic stem cells, where it causes post-transcriptional attenuation of Nanog and LRH1. Stem Cells. 2008; 26(1): 17-29.
34. Mah SM, Buske C, Humphries RK, Kuchenbauer F. miRNA*: a passenger stranded in RNA-induced silencing complex? Crit Rev Eukaryot Gene Expr. 2010; 20(2): 141-8.
35. Lujambio A, Lowe SW. The microcosmos of cancer. Nature. 2012; 482(7385): 347-55.
36. Zhang T, Luo Y, Wang T, Yang JY. MicroRNA-297b-5p/3p target Mllt3/Af9 to suppress lymphoma cell proliferation, migration and invasion in vitro and tumor growth in nude mice. Leuk Lymphoma. 2012; 53(10): 2033-40.
37. Zhang Y, Yang P, Sun T, et al. miR-126 and miR-126* repress recruitment of mesenchymal stem cells and inflammatory monocytes to inhibit breast cancer metastasis. Nature cell biology. 2013; 15(3): 284-94.
38. Yang JS, Phillips MD, Betel D, et al. Widespread regulatory activity of vertebrate microRNA* species. RNA. 2011; 17(2): 312-26.
39. Guo L, Lu Z. The fate of miRNA* strand through evolutionary analysis: implication for degradation as merely carrier strand or potential regulatory molecule? PLoS One. 2010; 5(6): e11387.
40. Khvorova A, Reynolds A, Jayasena SD. Functional siRNAs and miRNAs exhibit strand bias. Cell. 2003; 115(2): 209-16.
41. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD. Asymmetry in the assembly of the RNAi enzyme complex. Cell. 2003; 115(2): 199-208.
42. Griffiths-Jones S, Hui JH, Marco A, Ronshaugen M. MicroRNA evolution by arm switching. EMBO reports. 2011; 12(2): 172-7.
43. Marco A, Macpherson JI, Ronshaugen M, Griffiths-Jones S. MicroRNAs from the same precursor have different targeting properties. Silence. 2012; 3(1):8.
44. Noland CL, Doudna JA. Multiple sensors ensure guide strand selection in human RNAi pathways. RNA. 2013; 19(5): 639-48.
45. Miller JP, Yeh N, Vidal A, Koff A. Interweaving the cell cycle machinery with cell differentiation. Cell Cycle. 2007;6(23):2932-8.
46. Wang Y, Blelloch R. Cell cycle regulation by MicroRNAs in embryonic stem cells. Cancer Res. 2009; 69(10): 4093-6.
47. Ghule PN, Medina R, Lengner CJ, et al. Reprogramming the pluripotent cell cycle: restoration of an abbreviated G1 phase in human induced pluripotent stem (iPS) cells. J Cell Physiol. 2011; 226(5): 1149-56.
48. Stadler B, Ivanovska I, Mehta K, et al. Characterization of microRNAs involved in embryonic stem cell states. Stem Cells Dev. 2010; 19(7): 935-50.
49. Kuo CH, Deng JH, Deng Q, Ying SY. A novel role of miR-302/367 in reprogramming. Biochem Biophys Res Commun. 2012; 417(1): 11-6.
50. Li Z, Yang CS, Nakashima K, Rana TM. Small RNA-mediated regulation of iPS cell generation. EMBO J. 2011; 30(5): 823-34.
51. Miyoshi N, Ishii H, Nagano H, et al. Reprogramming of mouse and human cells to pluripotency using mature microRNAs. Cell Stem Cell. 2011; 8(6): 633-8.
52. Choi YJ, Lin CP, Ho JJ, et al. miR-34 miRNAs provide a barrier for somatic cell reprogramming. Nat Cell Biol. 2011; 13(11): 1353-60.
53. Viswanathan SR, Daley GQ, Gregory RI. Selective blockade of microRNA processing by Lin28. Science. 2008; 320(5872): 97-100.
54. Suzuki HI, Yamagata K, Sugimoto K, Iwamoto T, Kato S, Miyazono K. Modulation of microRNA processing by p53. Nature. 2009; 460(7254): 529-33.