Акбердин И.Р., Иванисенко Н.В., Казанцев Ф.В., Ощепкова Е.А., Омельянчук Н.А., Матушкин Ю.Г., Афонников Д.А.
Моделирование механизмов регуляции поддержания плюрипотентности эмбриональных стволовых клеток: кинетический и стохастический подходы
Математическая биология и биоинформатика. 2014;9(2):504-517.
doi: 10.17537/2014.9.504.
Список литературы
- Medvedev SP, Shevchenko AI, Sukhikh GT, Zakiian SM. Indutsirovannye pliuripotentnye stvolovye kletki (Induced pluripotent stem cells). Ed. Vlasova V.V. Novosibirsk; 2014. 368 p. (in Russ.).
- Jaenisch R, Young R. Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell. 2008;132(4):567-582. doi: 10.1016/j.cell.2008.01.015
- Graf T, Stadtfeld M. Heterogeneity of embryonic and adult stem cells. Cell Stem Cell. 2008;3(5):480-483. doi: 10.1016/j.stem.2008.10.007
- MacArthur BD, Lemischka IR. Statistical mechanics of pluripotency. Cell. 2013;154(3):484-489. doi: 10.1016/j.cell.2013.07.024
- Hayashi K, Lopes SM, Tang F, Surani MA. Dynamic equilibrium and heterogeneity of mouse pluripotent stem cells with distinct functional and epigenetic states. Cell Stem Cell. 2008;3(4):391-401. doi: 10.1016/j.stem.2008.07.027
- Torres-Padilla ME, Chambers I. Transcription factor heterogeneity in pluripotent stem cells: a stochastic advantage. Development. 2014;141(11):2173-2181. doi: 10.1242/dev.102624
- Akberdin IR, Kazantsev FV, Ermak TV, Timonov VS, Khlebodarova TM, Likhoshvai VA. In Silico Cell: Challenges and Perspectives. Matematicheskaya biologiya i bioinformatika (Mathematical Biology and Bioinformatics). 2013;8(1):295-315 (in Russ.). doi: 10.17537/2013.8.295
- Kalmar T, Lim C, Hayward P, Muñoz-Descalzo S, Nichols J, Garcia-Ojalvo J, Martinez Arias A. Regulated fluctuations in Nanog expression mediate cell fate decisions in embryonic stem cells. PLoS Biol. 2009;7(7):e1000149. doi: 10.1371/journal.pbio.1000149
- Glauche I, Herberg M, Roeder I. Nanog variability and pluripotency regulation of embryonic stem cells-insights from a mathematical model analysis. PLoS One. 2010;5(6):e11238. doi: 10.1371/journal.pone.0011238
- Wu J, Tzanakakis ES. Distinct allelic patterns of Nanog expression impart embryonic stem cell population heterogeneity. PLoS Comp. Biol. 2013;9(7):e1003140.
- Chickarmane V, Olariu V, Peterson C. Probing the role of stochasticity in a model of the embryonic stem cell-heterogeneous gene expression and reprogramming efficiency. BMC Syst. Biol. 2012;6(1):98. doi: 10.1186/1752-0509-6-98
- Chickarmane V, Troein C, Nuber UA, Sauro HM, Peterson C. Transcriptional dynamics of the embryonic stem cell switch. PLoS Comp. Biol. 2006;2(9):e123.
- Chickarmane V, Peterson C. A computational model for understanding stem cell, trophectoderm and endoderm lineage determination. PLoS One. 2008;3(10):e3478. doi: 10.1371/journal.pone.0003478
- Buchler NE, Gerland U, Hwa T. On schemes of combinatorial transcription logic. PNAS. 2003;100(9):5136-5141. doi: 10.1073/pnas.0930314100
- Ying QL, Wray J, Nichols J, Batlle-Morera L, Doble B, Woodgett J, Cohen P, Smith A. The ground state of embryonic stem cell self-renewal. Nature. 2008;453(7194):519-523. doi: 10.1038/nature06968
- Adachi K, Schöler HR. Directing reprogramming to pluripotency by transcription factors. Curr. Opin. Gen.&Dev. 2012;22(5):416-422.
- Fidalgo M, Faiola F, Pereira CF, Ding J, Saunders A, Gingold J, Schaniel C, Lemischka IR, Silva JC, Wang J. Zfp281 mediates Nanog autorepression through recruitment of the NuRD complex and inhibits somatic cell reprogramming. PNAS. 2012;109(40):16202-16207. doi: 10.1073/pnas.1208533109
- Wu J, Tzanakakis ES. Contribution of stochastic partitioning at human embryonic stem cell division to NANOG heterogeneity. PloS One. 2012;7(11):e50715. doi: 10.1371/journal.pone.0050715
- Navarro P, Festuccia N, Colby D, Gagliardi A, Mullin NP, Zhang W, Karwacki-Neisius V, Osorno R, Kelly D, Robertson M, Chambers I. OCT4/SOX2-independent Nanog autorepression modulates heterogeneous Nanog gene expression in mouse ES cells. The EMBO J. 2012;31(24):4547-4562. doi: 10.1038/emboj.2012.321
- Singh AM, Hamazaki T, Hankowski KE, Terada N. A heterogeneous expression pattern for Nanog in embryonic stem cells. Stem Cells. 2007;25(10):2534-2542. doi: 10.1634/stemcells.2007-0126
- Karwacki-Neisius V, Göke J, Osorno R, Halbritter F, Ng JH, Weiße AY, Wong FCK, Gagliardi A, Mullin NP, Festuccia N, Colby D, Tomlinson SR, Ng HH, Chambers I. Reduced Oct4 expression directs a robust pluripotent state with distinct signaling activity and increased enhancer occupancy by Oct4 and Nanog. Cell Stem Cell. 2013;12(5):531-545. doi: 10.1016/j.stem.2013.04.023
- Thomson M, Liu SJ, Zou LN, Smith Z, Meissner A, Ramanathan S. Pluripotency factors in embryonic stem cells regulate differentiation into germ layers. Cell. 2011;145(6):875-889. doi: 10.1016/j.cell.2011.05.017
- Abranches E, Bekman E, Henrique D. Generation and characterization of a novel mouse embryonic stem cell line with a dynamic reporter of Nanog expression. PloS One. 2013;8(3):e59928. doi: 10.1371/journal.pone.0059928
- Saxe JP, Tomilin A, Schöler HR, Plath K, Huang J. Post-translational regulation of Oct4 transcriptional activity. PloS One. 2009;4(2):e4467. doi: 10.1371/journal.pone.0004467
- Likhoshvai V, Ratushny A. Generalized hill function method for modeling molecular processes. J. Bioinform. Comput. Biol. 2007;5(02b):521-531. doi: 10.1142/S0219720007002837
- Gillespie DT. Stochastic simulation of chemical kinetics. Annu. Rev. Phys. Chem. 2007;58:35-55. doi: 10.1146/annurev.physchem.58.032806.104637
- Gillespie DT. Simulation methods in systems biology. In: Formal Methods for Computational Systems Biology. Eds. Bernardo M., Degano P., Zavattaro G. Springer Berlin Heidelberg; 2008. P. 125-167. doi: 10.1007/978-3-540-68894-5_5
- Rohr C, Marwan W, Heiner M. Snoopy - a unifying Petri net framework to investigate biomolecular networks. Bioinformatics. 2010;26(7):974-975. doi: 10.1093/bioinformatics/btq050
- Gillespie DT. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 1977;81(25):2340-2361. doi: 10.1021/j100540a008
- Papapetrou EP, Tomishima MJ, Chambers SM, Mica Y, Reed E, Menon J, Tabar V, Mo Q, Studer L, Sadelain M. Stoichiometric and temporal requirements of Oct4, Sox2, Klf4, and c-Myc expression for efficient human iPSC induction and differentiation. PNAS. 2009;106(31):12759-12764. doi: 10.1073/pnas.0904825106
- Suzuki A, Raya Á, Kawakami Y, Morita M, Matsui T, Nakashima K, Gage FH, Rodríguez-Esteban C, Belmonte JCI. Nanog binds to Smad1 and blocks bone morphogenetic protein-induced differentiation of embryonic stem cells. PNAS. 2006;103(27):10294-10299. doi: 10.1073/pnas.0506945103
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