MicroRNA signatures of iPSCs and endoderm-derived tissues

Anokye-Danso, 2011, Highly efficient miRNA-mediated reprogramming of mouse and human somatic cells to pluripotency, Cell Stem Cell, 8, 376, 10.1016/j.stem.2011.03.001 Borowiak, 2009, Small molecules efficiently direct endodermal differentiation of mouse and human embryonic stem cells, Cell Stem Cell, 4, 348, 10.1016/j.stem.2009.01.014 Chambers, 2007, Nanog safeguards pluripotency and mediates germline development, Nature, 450, 1230, 10.1038/nature06403 Chen, 2007, Defining embryonic stem cell identity using differentiation-related microRNAs and their potential targets, Mamm. Genome, 18, 316, 10.1007/s00335-007-9032-6 Chen, 2005, Real-time quantification of microRNAs by stem-loop RT-PCR, Nucleic Acids Res., 33, e179, 10.1093/nar/gni178 Choi, 2011, MiR-34 miRNAs provide a barrier for somatic cell reprogramming, Nat. Cell Biol., 13, 1353, 10.1038/ncb2366 Christodoulou, 2011, Mouse ES and iPS cells can form similar definitive endoderm despite differences in imprinted genes, J. Clin. Invest., 121, 2313, 10.1172/JCI43853 D’Amour, 2005, Efficient differentiation of human embryonic stem cells to definitive endoderm, Nat. Biotechnol., 23, 1534, 10.1038/nbt1163 Delaloy, 2010, MicroRNA-9 coordinates proliferation and migration of human embryonic stem cell-derived neural progenitors, Cell Stem Cell, 6, 323, 10.1016/j.stem.2010.02.015 Deutsch, 2001, A bipotential precursor population for pancreas and liver within the embryonic endoderm, Development, 128, 871, 10.1242/dev.128.6.871 Esau, 2006, MiR-122 regulation of lipid metabolism revealed by in vivo antisense targeting, Cell Metab., 3, 87, 10.1016/j.cmet.2006.01.005 Filipowicz, 2008, Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?, Nat. Rev. Genet., 9, 102, 10.1038/nrg2290 Gentleman, 2005 Gregory, 2008, The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1, Nat. Cell Biol., 10, 593, 10.1038/ncb1722 Grompe, 2003, Pancreatic–hepatic switches in vivo, Mech. Dev., 120, 99, 10.1016/S0925-4773(02)00336-2 Hinton, 2010, A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells, Stem Cells Dev., 19, 797, 10.1089/scd.2009.0224 Hobert, 2008, Gene regulation by transcription factors and microRNAs, Science, 319, 1785, 10.1126/science.1151651 Horb, 2003, Experimental conversion of liver to pancreas, Curr. Biol., 13, 105, 10.1016/S0960-9822(02)01434-3 Houbaviy, 2003, Embryonic stem cell-specific microRNAs, Dev. Cell, 5, 351, 10.1016/S1534-5807(03)00227-2 Ivey, 2008, MicroRNA regulation of cell lineages in mouse and human embryonic stem cells, Cell Stem Cell, 2, 219, 10.1016/j.stem.2008.01.016 Ivey, 2010, MicroRNAs as regulators of differentiation and cell fate decisions, Cell Stem Cell, 7, 36, 10.1016/j.stem.2010.06.012 Juan, 2009, Mir-214-dependent regulation of the polycomb protein Ezh2 in skeletal muscle and embryonic stem cells, Mol. Cell, 36, 61, 10.1016/j.molcel.2009.08.008 Judson, 2009, Embryonic stem cell-specific microRNAs promote induced pluripotency, Nat. Biotechnol., 27, 459, 10.1038/nbt.1535 Kloosterman, 2006, The diverse functions of microRNAs in animal development and disease, Dev. Cell, 11, 441, 10.1016/j.devcel.2006.09.009 Krützfeldt, 2005, Silencing of microRNAs in vivo with ‘antagomirs’, Nature, 438, 685, 10.1038/nature04303 Kubo, 2004, Development of definitive endoderm from embryonic stem cells in culture, Development, 131, 1651, 10.1242/dev.01044 Lagos-Quintana, 2002, Identification of tissue-specific microRNAs from mouse, Curr. Biol., 12, 735, 10.1016/S0960-9822(02)00809-6 Landgraf, 2007, A mammalian microRNA expression atlas based on small RNA library sequencing, Cell, 129, 1401, 10.1016/j.cell.2007.04.040 Lewis, 2003, Prediction of mammalian microRNA targets, Cell, 115, 787, 10.1016/S0092-8674(03)01018-3 Lowe, 2001, Genetic dissection of nodal function in patterning the mouse embryo, Development, 128, 1831, 10.1242/dev.128.10.1831 Marson, 2008, Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells, Cell, 134, 521, 10.1016/j.cell.2008.07.020 McGlinn, 2009, In ovo application of antagomiRs indicates a role for miR-196 in patterning the chick axial skeleton through Hox gene regulation, Proc. Natl. Acad. Sci. U.S.A., 106, 18610, 10.1073/pnas.0910374106 Melton, 2010, Opposing microRNA families regulate self-renewal in mouse embryonic stem cells, Nature, 463, 621, 10.1038/nature08725 Murakami, 2011, The progression of liver fibrosis is related with overexpression of the miR-199 and 200 families, PLoS ONE, 6, e16081, 10.1371/journal.pone.0016081 O’Loghlen, 2012, MicroRNA regulation of Cbx7 mediates a switch of polycomb orthologs during ESC differentiation, Cell Stem Cell, 10, 33, 10.1016/j.stem.2011.12.004 Poy, 2004, A pancreatic islet-specific microRNA regulates insulin secretion, Nature, 432, 226, 10.1038/nature03076 Roderburg, 2011, Micro-RNA profiling reveals a role for miR-29 in human and murine liver fibrosis, Hepatology, 53, 209, 10.1002/hep.23922 Rosa, 2009, The miR-430/427/302 family controls mesendodermal fate specification via species-specific target selection, Dev. Cell, 16, 517, 10.1016/j.devcel.2009.02.007 Samavarchi-Tehrani, 2010, Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming, Cell Stem Cell, 7, 64, 10.1016/j.stem.2010.04.015 Shen, 2000, Molecular basis of transdifferentiation of pancreas to liver, Nat. Cell Biol., 2, 879, 10.1038/35046522 Simion, 2010, MiR-495 and miR-218 regulate the expression of the Onecut transcription factors HNF-6 and OC-2, Biochem. Biophys. Res. Commun., 391, 293, 10.1016/j.bbrc.2009.11.052 Smyth, 2004, Linear models and empirical bayes methods for assessing differential expression in microarray experiments, Stat. Appl. Genet. Mol. Biol., 3, 10.2202/1544-6115.1027 Subramanyam, 2011, Multiple targets of miR-302 and miR-372 promote reprogramming of human fibroblasts to induced pluripotent stem cells, Nat. Biotechnol., 29, 443, 10.1038/nbt.1862 Tada, 2005, Characterization of mesendoderm: a diverging point of the definitive endoderm and mesoderm in embryonic stem cell differentiation culture, Development, 132, 4363, 10.1242/dev.02005 Takahashi, 2007, Induction of pluripotent stem cells from fibroblast cultures, Nat. Protoc., 2, 3081, 10.1038/nprot.2007.418 Takahashi, 2006, Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors, Cell, 126, 663, 10.1016/j.cell.2006.07.024 Tehler, 2011, The miR-10 microRNA precursor family, RNA Biol., 8, 728, 10.4161/rna.8.5.16324 Tripathi, 2011, Messenger RNA and microRNA profiling during early mouse EB formation, Gene Expr. Patterns, 11, 334, 10.1016/j.gep.2011.03.004 Tzur, 2008, MicroRNA expression patterns and function in endodermal differentiation of human embryonic stem cells, PLoS ONE, 3, e3726, 10.1371/journal.pone.0003726 van Rooij, 2008, Dysregulation of microRNAs after myocardial infarction reveals a role of miR-29 in cardiac fibrosis, Proc. Natl. Acad. Sci. U.S.A., 105, 13027, 10.1073/pnas.0805038105 Vincent, 2003, Cell fate decisions within the mouse organizer are governed by graded Nodal signals, Genes Dev., 17, 1646, 10.1101/gad.1100503 Wang, 2008, Embryonic stem cell-specific microRNAs regulate the G1-S transition and promote rapid proliferation, Nat. Genet., 40, 1478, 10.1038/ng.250 Yang, 2011, MicroRNAs modulate iPS cell generation, RNA, 17, 1451, 10.1261/rna.2664111 Yasunaga, 2005, Induction and monitoring of definitive and visceral endoderm differentiation of mouse ES cells, Nat. Biotechnol., 23, 1542, 10.1038/nbt1167 Zaret, 2008, Genetic programming of liver and pancreas progenitors: lessons for stem-cell differentiation, Nat. Rev. Genet., 9, 329, 10.1038/nrg2318