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Ultimately their genetics. However various genes get turned off at programmed times by methylation of the DNA while others get turned on at programmed times by demethylation of the DNA. The methylated/demethylated forms of the DNA are passed on to the stem cell's descendants so they "retain their programmed state" and thus their identity following differentiation. Some of this program control is influenced by the concentrations of various chemicals secreted by other cells in the vicinity of the stem cell or its descendants.

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