Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells

PLoS Computational Biology

Volumn 10, Issue 8, 2014, Pages

  Xu, Huilei ^a   Ang, Yen Sin ^a   Sevilla, Ana ^a   Lemischka, Ihor R ^a   Ma'ayan, Avi ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BODY FLUIDS; COMPUTER CIRCUITS; DATA INTEGRATION; FORECASTING; MAMMALS; NETWORK COMPONENTS; REVERSE ENGINEERING; SPECIFICATIONS; STEM CELLS; TOPOLOGY;

CELL-BE; CELL/B.E; CELL/BE; CONDITION; EXPRESSION LEVELS; GENES EXPRESSION; MICE EMBRYONIC STEM CELLS; PLURIPOTENCY; SELF RENEWAL; SINGLE CELLS;

GENE EXPRESSION;

OCTAMER TRANSCRIPTION FACTOR 4; TRANSCRIPTION FACTOR 7 LIKE 1; TRANSCRIPTION FACTOR NANOG; TRANSCRIPTION FACTOR SOX2;

ANIMAL CELL; ARTICLE; CELL CULTURE; CELL FATE; CELL LINEAGE; CELL SELF-RENEWAL; COMPUTER MODEL; COMPUTER PREDICTION; CONTROLLED STUDY; EMBRYO; EMBRYONIC STEM CELL; GENE EXPRESSION; GENE SILENCING; GENETIC ANALYSIS; MOUSE; NONHUMAN; PLURIPOTENT STEM CELL; PROTEIN FUNCTION; PROTEIN INTERACTION; RNA INTERFERENCE; VALIDATION STUDY; ANIMAL; CELL LINE; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENETICS; PHYSIOLOGY; REPRODUCIBILITY; SYSTEMS BIOLOGY;

ANIMALS; CELL LINE; COMPUTER SIMULATION; EMBRYONIC STEM CELLS; GENE EXPRESSION PROFILING; GENE KNOCKDOWN TECHNIQUES; GENE REGULATORY NETWORKS; MICE; PLURIPOTENT STEM CELLS; REPRODUCIBILITY OF RESULTS; SYSTEMS BIOLOGY;

EID: 84923692243     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003777     Document Type: Article

References (49)

1. Takahashi K, Yamanaka S, (2006) Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors Cell. 126: 663–676.
2. Park I-H, Zhao R, West JA, Yabuuchi A, Huo H, et al. (2008) Reprogramming of human somatic cells to pluripotency with defined factors. Nature 451: 141–146.
3. Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, et al. (2007) Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells. Science 318: 1917–1920.
4. Young RA, (2011) Control of the embryonic stem cell state. Cell 144: 940–954.
5. Setty Y, (2014) In-silico models of stem cell and developmental systems. Theoretical Biology and Medical Modelling 11: 1.
6. Li C, Wang J, (2013) Quantifying cell fate decisions for differentiation and reprogramming of a human stem cell network: landscape and biological paths. PLoS computational biology 9: e1003165.
7. Herberg M, Kalkan T, Glauche I, Smith A, Roeder I, (2014) A Model-Based Analysis of Culture-Dependent Phenotypes of mESCs. PloS one 9: e92496.
8. MacArthur BD, Please CP, Oreffo ROC, (2008) Stochasticity and the Molecular Mechanisms of Induced Pluripotency. PLoS ONE 3: e3086.
9. Dunn S-J, Martello G, Yordanov B, Emmott S, Smith AG, (2014) Defining an essential transcription factor program for naïve pluripotency. Science 344: 1156–1160.
10. Lee Y, Zhou Q, (2013) Co-regulation in embryonic stem cells via context-dependent binding of transcription factors. Bioinformatics 29: 2162–2168.
11. Dowell KG, Simons AK, Bai H, Kell B, Wang ZZ, et al. (2014) Novel Insights into Embryonic Stem Cell Self-Renewal Revealed Through Comparative Human and Mouse Systems Biology Networks. STEM CELLS 32: 1161–1172.
12. Karlebach G, Shamir R, (2012) Constructing Logical Models of Gene Regulatory Networks by Integrating Transcription Factor–DNA Interactions with Expression Data: An Entropy-Based Approach. Journal of Computational Biology 19: 30–41.
13. Xu H, Baroukh C, Dannenfelser R, Chen EY, Tan CM, et al. (2013) ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. Database 2013: bat045.
14. Xu H, Baroukh C, Dannenfelser R, Chen EY, Tan CM, et al. (2013) ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. Database: the journal of biological databases and curation 2013: bat045.
15. Narsinh KH, Sun N, Sanchez-Freire V, Lee AS, Almeida P, et al. (2011) Single cell transcriptional profiling reveals heterogeneity of human induced pluripotent stem cells. J Clin Invest 121: 1217–1221.
16. Carter MG, Stagg CA, Falco G, Yoshikawa T, Bassey UC, et al. (2008) An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells. Gene Expression Patterns 8: 181–198.
17. Pieprzyk M, High H (2009) Fluidigm Dynamic Arrays provide a platform for single-cell gene expression analysis. Nature Methods 9: : iii–iv.
18. Ying QL, Wray J, Nichols J, Batlle-Morera L, Doble B, et al. (2008) The ground state of embryonic stem cell self-renewal. Nature 453: 519–523.
19. Dunn S-J, Martello G, Yordanov B, Emmott S, Smith A, (2014) Defining an essential transcription factor program for naïve pluripotency. Science 344: 1156–1160.
20. Martinez Arias A, Brickman JM, (2011) Gene expression heterogeneities in embryonic stem cell populations: origin and function. Curr Opin Cell Biol 2: 650–6 doi: 10.1016/j.ceb.2011.09.007
21. Wray J, Kalkan T, Smith AG, (2010) The ground state of pluripotency. Biochem Soc Trans 38: 1027–1032.
22. Joksimovic M, Yun BA, Kittappa R, Anderegg AM, Chang WW, et al. (2009) Wnt antagonism of Shh facilitates midbrain floor plate neurogenesis. Nat Neurosci 12: 125–131.
23. Prakash N, Wurst W, (2007) A Wnt signal regulates stem cell fate and differentiation in vivo. Neurodegener Dis 4: 333–338.
24. Tang F, Barbacioru C, Bao S, Lee C, Nordman E, et al. (2010) Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. Cell Stem Cell 6: 468–478.
25. Ivanova N, Dobrin R, Lu R, Kotenko I, Levorse J, et al. (2006) Dissecting self-renewal in stem cells with RNA interference. Nature 442: 533–538.
26. Kauffman SA, (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. Journal of Theoretical Biology 22: 437–467.
27. Li S, Assmann SM, Albert R, eacute ka, (2006) Predicting Essential Components of Signal Transduction Networks: A Dynamic Model of Guard Cell Abscisic Acid Signaling. PLoS Biology 4: e312.
28. Schmidt M, Lipson H, (2009) Distilling free-form natural laws from experimental data. Science 324: 81–85.
29. Niwa H, Miyazaki J, Smith AG, (2000) Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat Genet 24: 372–376.
30. Pan G, Thomson JA, (2007) Nanog and transcriptional networks in embryonic stem cell pluripotency. Cell Res 17: 42–49.
31. Okumura-Nakanishi S, Saito M, Niwa H, Ishikawa F, (2005) Oct-3/4 and Sox2 regulate Oct-3/4 gene in embryonic stem cells. J Biol Chem 280: 5307–5317.
32. Feng B, Jiang J, Kraus P, Ng JH, Heng JC, et al. (2009) Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb. Nat Cell Biol 11: 197–203.
33. Pesce M, Scholer HR, (2001) Oct-4: gatekeeper in the beginnings of mammalian development. Stem Cells 19: 271–278.
34. Kim JB, Sebastiano V, Wu G, Arauzo-Bravo MJ, Sasse P, et al. (2009) Oct4-induced pluripotency in adult neural stem cells. Cell 136: 411–419.
35. Hough SR, Clements I, Welch PJ, Wiederholt KA, (2006) Differentiation of mouse embryonic stem cells after RNA interference-mediated silencing of OCT4 and Nanog. Stem Cells 24: 1467–1475.
36. Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, et al. (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122: 947–956.
37. Boyer LA, Plath K, Zeitlinger J, Brambrink T, Medeiros LA, et al. (2006) Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441: 349–353.
38. Loh YH, Wu Q, Chew JL, Vega VB, Zhang W, et al. (2006) The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet 38: 431–440.
39. Cole MF, Johnstone SE, Newman JJ, Kagey MH, Young RA, (2008) Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells. Genes Dev 22: 746–755.
40. Yi F, Pereira L, Merrill BJ, (2008) Tcf3 functions as a steady-state limiter of transcriptional programs of mouse embryonic stem cell self-renewal. Stem Cells 26: 1951–1960.
41. Lu R, Markowetz F, Unwin RD, Leek JT, Airoldi EM, et al. (2009) Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature 462: 358–362.
42. Velkey JM, O'Shea KS, (2003) Oct4 RNA interference induces trophectoderm differentiation in mouse embryonic stem cells. genesis 37: 18–24.
43. MacArthur BD, Sevilla A, Lenz M, Maller F-J, Schuldt BM, et al. (2012) Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity. Nat Cell Biol 14: 1139–47 doi: 10.1038/ncb2603
44. Theunissen TW, van Oosten AL, Castelo-Branco G, Hall J, Smith A, et al. (2011) Nanog overcomes reprogramming barriers and induces pluripotency in minimal conditions. Curr Biol 21: 65–71.
45. Ang Y-S, Tsai S-Y, Lee D-F, Monk J, Su J, et al. (2011) Wdr5 Mediates Self-Renewal and Reprogramming via the Embryonic Stem Cell Core Transcriptional Network. Cell 145: 183–197.
46. Robertson E, Bradley A, Kuehn M, Evans M, (1986) Germ-line transmission of genes introduced into cultured pluripotential cells by retroviral vector. 323: 445–8.
47. Ying QL, Smith AG, (2003) Defined conditions for neural commitment and differentiation. Methods Enzymol 365: 327–341.
48. Ang Y-S, Tsai S-Y, Lee D-F, Monk J, Su J, et al. (2011) Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell 145: 183–197.
49. Chew JL, Loh YH, Zhang W, Chen X, Tam WL, et al. (2005) Reciprocal transcriptional regulation of Pou5f1 and Sox2 via the Oct4/Sox2 complex in embryonic stem cells. Mol Cell Biol 25: 6031–6046.