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Volumn 32, Issue 9, 2014, Pages 2360-2372

SRNA-seq analysis of human embryonic stem cells and definitive endoderm reveals differentially expressed micrornas and novel isomirs with distinct targets

Author keywords

Differentiation; Embryonic stem cells; miRNA; Pluripotency

Indexed keywords

MICRORNA; TRANSCRIPTION FACTOR OTX2; TRANSFER RNA; SMALL INTERFERING RNA;

EID: 84906265678     PISSN: 10665099     EISSN: 15494918     Source Type: Journal    
DOI: 10.1002/stem.1739     Document Type: Article
Times cited : (30)

References (48)
  • 1
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: Target recognition and regulatory functions
    • Bartel DP,. MicroRNAs: Target recognition and regulatory functions. Cell 2009; 136: 215-233.
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 2
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • Bartel DP,. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 2004; 116: 281-297.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 3
    • 77952368550 scopus 로고    scopus 로고
    • Mammalian microRNAs: Experimental evaluation of novel and previously annotated genes
    • Chiang HR, Schoenfeld LW, Ruby JG, et al. Mammalian microRNAs: Experimental evaluation of novel and previously annotated genes. Genes Dev 2010; 24: 992-1009.
    • (2010) Genes Dev , vol.24 , pp. 992-1009
    • Chiang, H.R.1    Schoenfeld, L.W.2    Ruby, J.G.3
  • 4
    • 77955049511 scopus 로고    scopus 로고
    • Emerging roles of microRNAs in the control of embryonic stem cells and the generation of induced pluripotent stem cells
    • Mallanna SK, Rizzino A,. Emerging roles of microRNAs in the control of embryonic stem cells and the generation of induced pluripotent stem cells. Dev Biol 2010; 344: 16-25.
    • (2010) Dev Biol , vol.344 , pp. 16-25
    • Mallanna, S.K.1    Rizzino, A.2
  • 5
    • 79960015284 scopus 로고    scopus 로고
    • MicroRNA regulation of embryonic stem cell self-renewal and differentiation
    • Melton C, Blelloch R,. MicroRNA regulation of embryonic stem cell self-renewal and differentiation. Adv Exp Med Biol 2010; 695: 105-117.
    • (2010) Adv Exp Med Biol , vol.695 , pp. 105-117
    • Melton, C.1    Blelloch, R.2
  • 6
    • 56749091922 scopus 로고    scopus 로고
    • Embryonic stem cell-specific microRNAs regulate the G1-S transition and promote rapid proliferation
    • Wang Y, Baskerville S, Shenoy A, et al. Embryonic stem cell-specific microRNAs regulate the G1-S transition and promote rapid proliferation. Nat Genet 2008; 40: 1478-1483.
    • (2008) Nat Genet , vol.40 , pp. 1478-1483
    • Wang, Y.1    Baskerville, S.2    Shenoy, A.3
  • 7
    • 77954201278 scopus 로고    scopus 로고
    • A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells
    • Hinton A, Afrikanova I, Wilson M, et al. A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells. Stem Cells Dev 2010; 19: 797-807.
    • (2010) Stem Cells Dev , vol.19 , pp. 797-807
    • Hinton, A.1    Afrikanova, I.2    Wilson, M.3
  • 8
    • 39749140336 scopus 로고    scopus 로고
    • MicroRNA regulation of cell lineages in mouse and human embryonic stem cells
    • Ivey KN, Muth A, Arnold J, et al. MicroRNA regulation of cell lineages in mouse and human embryonic stem cells. Cell Stem Cell 2008; 2: 219-229.
    • (2008) Cell Stem Cell , vol.2 , pp. 219-229
    • Ivey, K.N.1    Muth, A.2    Arnold, J.3
  • 9
    • 65249093130 scopus 로고    scopus 로고
    • MiR-375 maintains normal pancreatic alpha- and beta-cell mass
    • Poy MN, Hausser J, Trajkovski M, et al. miR-375 maintains normal pancreatic alpha- and beta-cell mass. Proc Natl Acad Sci USA 2009; 106: 5813-5818.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 5813-5818
    • Poy, M.N.1    Hausser, J.2    Trajkovski, M.3
  • 10
    • 64549094131 scopus 로고    scopus 로고
    • The miR-430/427/302 family controls mesendodermal fate specification via species-specific target selection
    • Rosa A, Spagnoli FM, Brivanlou AH,. The miR-430/427/302 family controls mesendodermal fate specification via species-specific target selection. Dev Cell 2009; 16: 517-527.
    • (2009) Dev Cell , vol.16 , pp. 517-527
    • Rosa, A.1    Spagnoli, F.M.2    Brivanlou, A.H.3
  • 11
    • 84866420583 scopus 로고    scopus 로고
    • From pluripotency to islets: MiRNAs as critical regulators of human cellular differentiation
    • Hinton A, Hunter S, Reyes G, et al. From pluripotency to islets: miRNAs as critical regulators of human cellular differentiation. Adv Genet 2012; 79: 1-34.
    • (2012) Adv Genet , vol.79 , pp. 1-34
    • Hinton, A.1    Hunter, S.2    Reyes, G.3
  • 12
    • 76249119007 scopus 로고    scopus 로고
    • Opposing microRNA families regulate self-renewal in mouse embryonic stem cells
    • Melton C, Judson RL, Blelloch R,. Opposing microRNA families regulate self-renewal in mouse embryonic stem cells. Nature 2010; 463: 621-626.
    • (2010) Nature , vol.463 , pp. 621-626
    • Melton, C.1    Judson, R.L.2    Blelloch, R.3
  • 13
    • 0034794417 scopus 로고    scopus 로고
    • Feeder-free growth of undifferentiated human embryonic stem cells
    • Xu C, Inokuma MS, Denham J, et al. Feeder-free growth of undifferentiated human embryonic stem cells. Nat Biotechnol 2001; 19: 971-974.
    • (2001) Nat Biotechnol , vol.19 , pp. 971-974
    • Xu, C.1    Inokuma, M.S.2    Denham, J.3
  • 14
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker IL,. Vienna RNA secondary structure server. Nucleic Acids Res 2003; 31: 3429-3431.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 15
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • McCaskill JS,. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 1990; 29: 1105-1119.
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.S.1
  • 16
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker M, Stiegler P,. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 1981; 9: 133-148.
    • (1981) Nucleic Acids Res , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2
  • 17
    • 77949572066 scopus 로고    scopus 로고
    • Faster computation of exact RNA shape probabilities
    • Janssen S, Giegerich R,. Faster computation of exact RNA shape probabilities. Bioinformatics 2010; 26: 632-639.
    • (2010) Bioinformatics , vol.26 , pp. 632-639
    • Janssen, S.1    Giegerich, R.2
  • 18
    • 32544440797 scopus 로고    scopus 로고
    • RNAshapes: An integrated RNA analysis package based on abstract shapes
    • Steffen P, Voss B, Rehmsmeier M, et al. RNAshapes: An integrated RNA analysis package based on abstract shapes. Bioinformatics 2006; 22: 500-503.
    • (2006) Bioinformatics , vol.22 , pp. 500-503
    • Steffen, P.1    Voss, B.2    Rehmsmeier, M.3
  • 19
    • 0034708122 scopus 로고    scopus 로고
    • The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans
    • Reinhart BJ, Slack FJ, Basson M, et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 2000; 403: 901-906.
    • (2000) Nature , vol.403 , pp. 901-906
    • Reinhart, B.J.1    Slack, F.J.2    Basson, M.3
  • 20
    • 0024829771 scopus 로고
    • Optimized use of the firefly luciferase assay as a reporter gene in mammalian cell lines
    • Brasier AR, Tate JE, Habener JF,. Optimized use of the firefly luciferase assay as a reporter gene in mammalian cell lines. Biotechniques 1989; 7: 1116-1122.
    • (1989) Biotechniques , vol.7 , pp. 1116-1122
    • Brasier, A.R.1    Tate, J.E.2    Habener, J.F.3
  • 21
    • 28644448149 scopus 로고    scopus 로고
    • Efficient differentiation of human embryonic stem cells to definitive endoderm
    • D'Amour KA, Agulnick AD, Eliazer S, et al. Efficient differentiation of human embryonic stem cells to definitive endoderm. Nat Biotechnol 2005; 23: 1534-1541.
    • (2005) Nat Biotechnol , vol.23 , pp. 1534-1541
    • D'Amour, K.A.1    Agulnick, A.D.2    Eliazer, S.3
  • 22
    • 79959805164 scopus 로고    scopus 로고
    • MiRWalk - Database: Prediction of possible miRNA binding sites by "walking" the genes of three genomes
    • Dweep H, Sticht C, Pandey P, et al. miRWalk-Database: Prediction of possible miRNA binding sites by "walking" the genes of three genomes. J Biomed Inform 2011; 44: 839-847.
    • (2011) J Biomed Inform , vol.44 , pp. 839-847
    • Dweep, H.1    Sticht, C.2    Pandey, P.3
  • 23
    • 48449091318 scopus 로고    scopus 로고
    • Comprehensive microRNA profiling reveals a unique human embryonic stem cell signature dominated by a single seed sequence
    • Laurent LC, Chen J, Ulitsky I, et al. Comprehensive microRNA profiling reveals a unique human embryonic stem cell signature dominated by a single seed sequence. Stem Cells 2008; 26: 1506-1516.
    • (2008) Stem Cells , vol.26 , pp. 1506-1516
    • Laurent, L.C.1    Chen, J.2    Ulitsky, I.3
  • 24
    • 2942534403 scopus 로고    scopus 로고
    • Human embryonic stem cells express a unique set of microRNAs
    • Suh MR, Lee Y, Kim JY, et al. Human embryonic stem cells express a unique set of microRNAs. Dev Biol 2004; 270: 488-498.
    • (2004) Dev Biol , vol.270 , pp. 488-498
    • Suh, M.R.1    Lee, Y.2    Kim, J.Y.3
  • 25
    • 59449100501 scopus 로고    scopus 로고
    • The miR-302-367 cluster as a potential stemness regulator in ESCs
    • Barroso-del Jesus A, Lucena-Aguilar G, Menendez P,. The miR-302-367 cluster as a potential stemness regulator in ESCs. Cell Cycle 2009; 8: 394-398.
    • (2009) Cell Cycle , vol.8 , pp. 394-398
    • Barroso-Del Jesus, A.1    Lucena-Aguilar, G.2    Menendez, P.3
  • 26
    • 79955649501 scopus 로고    scopus 로고
    • The Nodal inhibitor Lefty is negatively modulated by the microRNA miR-302 in human embryonic stem cells
    • Barroso-delJesus A, Lucena-Aguilar G, Sanchez L, et al. The Nodal inhibitor Lefty is negatively modulated by the microRNA miR-302 in human embryonic stem cells. FASEB J 2011; 25: 1497-1508.
    • (2011) FASEB J , vol.25 , pp. 1497-1508
    • Barroso-Deljesus, A.1    Lucena-Aguilar, G.2    Sanchez, L.3
  • 27
    • 53549133376 scopus 로고    scopus 로고
    • Oct4/Sox2-regulated miR-302 targets cyclin D1 in human embryonic stem cells
    • Card DA, Hebbar PB, Li L, et al. Oct4/Sox2-regulated miR-302 targets cyclin D1 in human embryonic stem cells. Mol Cell Biol 2008; 28: 6426-6438.
    • (2008) Mol Cell Biol , vol.28 , pp. 6426-6438
    • Card, D.A.1    Hebbar, P.B.2    Li, L.3
  • 28
    • 78751640369 scopus 로고    scopus 로고
    • A regulatory circuitry comprised of miR-302 and the transcription factors OCT4 and NR2F2 regulates human embryonic stem cell differentiation
    • Rosa A, Brivanlou AH,. A regulatory circuitry comprised of miR-302 and the transcription factors OCT4 and NR2F2 regulates human embryonic stem cell differentiation. EMBO J 2011; 30: 237-248.
    • (2011) EMBO J , vol.30 , pp. 237-248
    • Rosa, A.1    Brivanlou, A.H.2
  • 29
    • 0028807157 scopus 로고
    • Forebrain and midbrain regions are deleted in Otx2-/- mutants due to a defective anterior neuroectoderm specification during gastrulation
    • Acampora D, Mazan S, Lallemand Y, et al. Forebrain and midbrain regions are deleted in Otx2-/- mutants due to a defective anterior neuroectoderm specification during gastrulation. Development 1995; 121: 3279-3290.
    • (1995) Development , vol.121 , pp. 3279-3290
    • Acampora, D.1    Mazan, S.2    Lallemand, Y.3
  • 30
    • 74849135201 scopus 로고    scopus 로고
    • The tumorigenicity of diploid and aneuploid human pluripotent stem cells
    • Blum B, Benvenisty N,. The tumorigenicity of diploid and aneuploid human pluripotent stem cells. Cell Cycle 2009; 8: 3822-3830.
    • (2009) Cell Cycle , vol.8 , pp. 3822-3830
    • Blum, B.1    Benvenisty, N.2
  • 31
    • 55049135859 scopus 로고    scopus 로고
    • MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries
    • Bar M, Wyman SK, Fritz BR, et al. MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem Cells 2008; 26: 2496-2505.
    • (2008) Stem Cells , vol.26 , pp. 2496-2505
    • Bar, M.1    Wyman, S.K.2    Fritz, B.R.3
  • 32
    • 16444373230 scopus 로고    scopus 로고
    • Activin A maintains pluripotency of human embryonic stem cells in the absence of feeder layers
    • Beattie GM, Lopez AD, Bucay N, et al. Activin A maintains pluripotency of human embryonic stem cells in the absence of feeder layers. Stem Cells 2005; 23: 489-495.
    • (2005) Stem Cells , vol.23 , pp. 489-495
    • Beattie, G.M.1    Lopez, A.D.2    Bucay, N.3
  • 33
    • 16244400050 scopus 로고    scopus 로고
    • TGFbeta/activin/nodal signaling is necessary for the maintenance of pluripotency in human embryonic stem cells
    • James D, Levine AJ, Besser D, et al. TGFbeta/activin/nodal signaling is necessary for the maintenance of pluripotency in human embryonic stem cells. Development 2005; 132: 1273-1282.
    • (2005) Development , vol.132 , pp. 1273-1282
    • James, D.1    Levine, A.J.2    Besser, D.3
  • 34
    • 73849085104 scopus 로고    scopus 로고
    • Identification of microRNAs regulated by activin A in human embryonic stem cells
    • Tsai ZY, Singh S, Yu SL, et al. Identification of microRNAs regulated by activin A in human embryonic stem cells. J Cell Biochem 2010; 109: 93-102.
    • (2010) J Cell Biochem , vol.109 , pp. 93-102
    • Tsai, Z.Y.1    Singh, S.2    Yu, S.L.3
  • 35
    • 78651293534 scopus 로고    scopus 로고
    • MiRBase: Integrating microRNA annotation and deep-sequencing data
    • (Database issue)
    • Kozomara A, Griffiths-Jones S,. miRBase: Integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011; 39 (Database issue): D152-157.
    • (2011) Nucleic Acids Res , vol.39
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 36
    • 78149332037 scopus 로고    scopus 로고
    • Complexity of the microRNA repertoire revealed by next-generation sequencing
    • Lee LW, Zhang S, Etheridge A, et al. Complexity of the microRNA repertoire revealed by next-generation sequencing. RNA 2010; 16: 2170-2180.
    • (2010) RNA , vol.16 , pp. 2170-2180
    • Lee, L.W.1    Zhang, S.2    Etheridge, A.3
  • 37
    • 41649106136 scopus 로고    scopus 로고
    • Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells
    • Morin RD, O'Connor MD, Griffith M, et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 2008; 18: 610-621.
    • (2008) Genome Res , vol.18 , pp. 610-621
    • Morin, R.D.1    O'Connor, M.D.2    Griffith, M.3
  • 38
    • 79955501601 scopus 로고    scopus 로고
    • ID4 imparts chemoresistance and cancer stemness to glioma cells by derepressing miR-9*-mediated suppression of SOX2
    • Jeon HM, Sohn YW, Oh SY, et al. ID4 imparts chemoresistance and cancer stemness to glioma cells by derepressing miR-9*-mediated suppression of SOX2. Cancer Res 2011; 71: 3410-3421.
    • (2011) Cancer Res , vol.71 , pp. 3410-3421
    • Jeon, H.M.1    Sohn, Y.W.2    Oh, S.Y.3
  • 39
    • 78650843340 scopus 로고    scopus 로고
    • MiRNAs regulate SIRT1 expression during mouse embryonic stem cell differentiation and in adult mouse tissues
    • (Albany NY)
    • Saunders LR, Sharma AD, Tawney J, et al. miRNAs regulate SIRT1 expression during mouse embryonic stem cell differentiation and in adult mouse tissues. Aging (Albany NY) 2010; 2: 415-431.
    • (2010) Aging , vol.2 , pp. 415-431
    • Saunders, L.R.1    Sharma, A.D.2    Tawney, J.3
  • 41
    • 34250877841 scopus 로고    scopus 로고
    • A mammalian microRNA expression atlas based on small RNA library sequencing
    • Landgraf P, Rusu M, Sheridan R, et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 2007; 129: 1401-1414.
    • (2007) Cell , vol.129 , pp. 1401-1414
    • Landgraf, P.1    Rusu, M.2    Sheridan, R.3
  • 42
    • 38149071979 scopus 로고    scopus 로고
    • Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
    • Ruby JG, Stark A, Johnston WK, et al. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res 2007; 17: 1850-1864.
    • (2007) Genome Res , vol.17 , pp. 1850-1864
    • Ruby, J.G.1    Stark, A.2    Johnston, W.K.3
  • 43
    • 0042442335 scopus 로고    scopus 로고
    • Embryonic stem cell-specific MicroRNAs
    • Houbaviy HB, Murray MF, Sharp PA,. Embryonic stem cell-specific MicroRNAs. Dev Cell 2003; 5: 351-358.
    • (2003) Dev Cell , vol.5 , pp. 351-358
    • Houbaviy, H.B.1    Murray, M.F.2    Sharp, P.A.3
  • 44
    • 0036546980 scopus 로고    scopus 로고
    • Neural induction, the default model and embryonic stem cells
    • Munoz-Sanjuan I, Brivanlou AH,. Neural induction, the default model and embryonic stem cells. Nat Rev Neurosci 2002; 3: 271-280.
    • (2002) Nat Rev Neurosci , vol.3 , pp. 271-280
    • Munoz-Sanjuan, I.1    Brivanlou, A.H.2
  • 45
    • 14244262504 scopus 로고    scopus 로고
    • Nodal inhibits differentiation of human embryonic stem cells along the neuroectodermal default pathway
    • Vallier L, Reynolds D, Pedersen RA,. Nodal inhibits differentiation of human embryonic stem cells along the neuroectodermal default pathway. Dev Biol 2004; 275: 403-421.
    • (2004) Dev Biol , vol.275 , pp. 403-421
    • Vallier, L.1    Reynolds, D.2    Pedersen, R.A.3
  • 46
    • 84866763591 scopus 로고    scopus 로고
    • Derivation of cerebellar neurons from human pluripotent stem cells
    • Unit 1H 5
    • Erceg S, Lukovic D, Moreno-Manzano V, et al. Derivation of cerebellar neurons from human pluripotent stem cells. Curr Protoc Stem Cell Biol 2012; Chapter 1:Unit 1H 5.
    • (2012) Curr Protoc Stem Cell Biol
    • Erceg, S.1    Lukovic, D.2    Moreno-Manzano, V.3
  • 47
    • 84859778293 scopus 로고    scopus 로고
    • MTOR signaling in growth control and disease
    • Laplante M, Sabatini DM,. mTOR signaling in growth control and disease. Cell 2012; 149: 274-293.
    • (2012) Cell , vol.149 , pp. 274-293
    • Laplante, M.1    Sabatini, D.M.2
  • 48
    • 77954945936 scopus 로고    scopus 로고
    • MTOR-mediated activation of p70 S6K induces differentiation of pluripotent human embryonic stem cells
    • Easley CAT, Ben-Yehudah A, Redinger CJ, et al. mTOR-mediated activation of p70 S6K induces differentiation of pluripotent human embryonic stem cells. Cell Reprogram 2010; 12: 263-273.
    • (2010) Cell Reprogram , vol.12 , pp. 263-273
    • Easley, C.A.T.1    Ben-Yehudah, A.2    Redinger, C.J.3


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