Defining embryonic stem cell identity using differentiation-related microRNAs and their potential targets

Springer Science and Business Media LLC - Tập 18 - Trang 316-327 - 2007
Caifu Chen1, Dana Ridzon1, Chung-Tien Lee2, Julie Blake1, Yongming Sun1, William M. Strauss2
1R&D, Applied Biosystems, Foster City, USA
2MCD Biology, University of Colorado, Boulder, USA

Tóm tắt

Defining the identity of embryonic stem (ES) cells in quantitative molecular terms is a prerequisite to understanding their functional characteristics. Little is known about the role of microRNAs (miRNAs) in the regulation of ES cell identity. Statistical analysis of miRNA expression revealed unique expression signatures that could definitively classify mouse ES (mES), embryoid bodies (mEB), and somatic tissues. Analysis of these data sets also provides further confirmation of the nonrestrictive expression of miRNAs during murine development. Using combined genome-wide expression analyses of both miRNAs and mRNAs, we observed both negative and positive correlations in gene expression between miRNAs and their predicted targets. ES-specific miRNAs were positively correlated with their predicted targets, suggesting that mES-specific miRNAs may have a different role or mechanism in regulating their targets in mES maintenance or differentiation. The concept of cellular identity has changed with technology; this study redefines cellular identity by a generic statistical method of known dimension.

Tài liệu tham khảo

Abeyta MJ, Clark AT, Rodriguez RT, Bodnar MS, Pera RA, et al. (2004) Unique gene expression signatures of independently-derived human embryonic stem cell lines. Hum Mol Genet 13(6):601–608 Babak T, Zhang W, Morris Q, Blencove BJ, Hoghes TR (2004) Probing microRNAs with microarrays: tissue specificity and functional inference. RNA 10(11):1813–1819 Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, et al. (2005) Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122(4):553–563 Bartel DP, Chen CZ (2004) Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat Rev Genet 5(5):396–400 Bernstein E, Kim SY, Carmell MA, Murchison EP, Alcorn H, et al. (2003) Dicer is essential for mouse development. Nat Genet 35(3):215–217 Bonnet D, Dick JE (1997) Human acute myeloid leukemia is organized as a hierarchy that originates from a primitive hematopoietic cell. Nat Med 3(7):730–737 Borchert G, Lanier W, Davidson BL (2006) RNA polymerase III transcribes human microRNAs. Nat Struct Mol Biol 13(12):1097–1101 Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, et al. (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122(6):947–956 Brennecke J, Stark A, Russell RB, Cohen SM (2005) Principles of microRNA-target recognition. PLoS Biol 3(3):e85 Cai X, Hagedorn CH, Cullen BR (2004) Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10(12):1957–1966 Carmell MA, Xuan Z, Zhang MQ, Hannon GJ (2002) The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev 16(21):2733–2742 Chambers I, Colby D, Robertson M, Nichols J, Lee S, et al. (2003) Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell 113(5):643–655 Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, et al. (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33(20):e179 Cheng LC, Tavazoie M, Doetsch F (2005) Stem cells: from epigenetics to microRNAs. Neuron 46(3):363–367 Clarke MF, Fuller M (2006) Stem cells and cancer: two faces of eve. Cell 124(6):1111–1115 Croce CM, Calin GA (2005) miRNAs, cancer, and stem cell division. Cell 122(1):6–7 Deo M, Yu JY, Chung KH, Tippens M, Turner DL (2006) Detection of mammalian microRNA expression by in situ hybridization with RNA oligonucleotides. Dev Dyn 235(9):2538–2548 Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95(25):14863–14868 Farh KK, Grimson A, Jan C, Lewis BP, Johnston WK, et al. (2005) The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science 310(5755):1817–1821 Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, et al. (2006) Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312(5770):75–79 Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34(Database issue):D140–D144 Hatfield SD, Shcherbata HR, Fischer KA, Nakahara K, Carthew RW, et al. (2005) Stem cell division is regulated by the microRNA pathway. Nature 435(7044):974–978 He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, et al. (2005) A microRNA polycistron as a potential human oncogene. Nature 435(7043):828–833 Hobert O (2004) Common logic of transcription factor and microRNA action. Trends Biochem Sci 29(9):462–468 Houbaviy HB, Murray MF, Sharp PA (2003) Embryonic stem cell-specific MicroRNAs. Dev Cell 5(2):351–358 Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, et al. (2001) A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293(5531):834–838 Ivanova NB, Dimos JT, Schaniel C, Hackney JA, Moore KA, et al. (2002) A stem cell molecular signature. Science 298(5593):601–604 Janowski B, Younger S, Hardy DB, Pam R, Huffman KE, et al. (2007) Activating gene expression in mammalian cells with promoter-targeted duplex RNAs. Nat Chem Biol 3(3):166–173 Ketting RF, Fischer SE, Bernstein E, Sijen T, Hannon GJ, et al. (2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev 15(20):2654–2659 Kim HK, Lee YS, Sivaprasad U, Malhotra A, Dutta A (2006) Muscle-specific microRNA miR-206 promotes muscle differentiation. J Cell Biol 174(5):677–687 Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, et al. (2002) Identification of tissue-specific microRNAs from mouse. Curr Biol 12(9):735–739 Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T (2003) New microRNAs from mouse and human. RNA 9(2):175–179 Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75(5):843–854 Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, et al. (2006) Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125(2):301–313 Lee Y, Kim M, Han J, Yeom KH, Lee S, et al. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23(20):4051–4060 Li LC, Okino S, Zhao H, Pookot D, Place RF, et al. (2006) Small dsRNAs induce transcriptional activation in human cells. Proc Natl Acad Sci U S A 103(46):17337–17342 Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, et al. (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433(7027):769–773 Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, et al. (2006) A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell 126(6):1203–1217 Mitsui K, Tokuzawa Y, Itoh H, Segawa K, Murakami M, et al. (2003) The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell 113(5):631–642 Murchison EP, Partridge JF, Tam OH, Cheloufi S, Hannon GJ, et al. (2005) Characterization of Dicer-deficient murine embryonic stem cells. Proc Natl Acad Sci U S A 102(34):12135–12140 Nichols J, Zevnik B, Anastassiadis K, Niwa H (1998) Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell 95(3):379–391 Olsen PH, Ambros V (1999) The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev Biol 216(2):671–680 Pardal R, Clarke MF, Morrison SJ (2003) Applying the principles of stem-cell biology to cancer. Nat Rev Cancer 3(12):895–902 Parizotto EA, Dunoyer P, Rahm N, Himber C, Voinnet O (2004) In vivo investigation of the transcription, processing, endonucleolytic activity, and functional relevance of the spatial distribution of a plant miRNA. Genes Dev 18(18):2237–2242 Pasquinelli AE, Ruvkun G (2002) Control of developmental timing by microRNAs and their targets. Annu Rev Cell Dev Biol 18:495–513 Ramalho-Santos M, Yoon S, Matsuzaki Y, Mulligan RC, Melton DA (2002) “Stemness”: transcriptional profiling of embryonic and adult stem cells. Science 298(5593):597–600 Sood P, Krek A, Zavolan M, Macino G, Rajewsky N (2006) Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci U S A 103(8):2746–2751 Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM (2005) Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3′ UTR evolution. Cell 123(6):1133–1146 Strauss WM, Chen C, Lee CT, Ridzon D (2006) Nonrestrictive developmental regulation of microRNA gene expression. Mamm Genome 17(8):833–840 Suh MR, Lee Y, Kim JY, Kim SK, Moon SH, et al. (2004) Human embryonic stem cells express a unique set of microRNAs. Dev Biol 270(2):488–498 Voorhoeve PM, le Sage C, Schrier M, Gillis AJ, Stoop H, et al. (2006) A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors. Cell 124(6):1169–1181 Wheeler G, Ntounia-Fousara S, Granda B, Rathjen T, Dalmay T (2006) Identification of new central nervous system specific mouse microRNAs. FEBS Lett 580(9):2195–2200 Wienholds E, Koudijs MJ, van Eeden FJ, Cuppen E, Plasterk RH (2003) The microRNA-producing enzyme Dicer1 is essential for zebrafish development. Nat Genet 35(3):217–218 Wightman B, Ha I, Ruvkun G (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75(5):855–862 Ying QL, Smith AG (2003) Defined conditions for neural commitment and differentiation. Methods Enzymol 365:327–341