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Fig. 4 | Theoretical Biology and Medical Modelling

Fig. 4

From: The organelle of differentiation in embryos: the cell state splitter

Fig. 4

Each cell has the same set of all genes encoded in the DNA (Red circle). All cells in an organism express a set of “Housekeeping” or “Reference” genes. These genes represent certain elements such as ribosomes and components of the DNA polymerases as well as some of the cytoskeletal elements (Brown circle). There are also genes for specific transcription factors that are required for turning off and on gene expression (Blue circle hatched). Transcriptions factor gene products (i.e., proteins that are transcription factors) may be expressed in many different cell types. Many transcriptions factors require the presence of specific regulatory cofactors (Pink circle) such as small RNAs to perform some (or even all) of their functions. Expression of specific transcription factors and their regulatory cofactors often changes during development and thereby changes function of tissue specific genes. Each cell also has a set of genes that are generally specific to the tissue type that the cell belongs to but which may also be expressed in other cell types (Green circle). A Regulon is the group of a single transcription factor and all of its regulatory cofactors required to regulate a specific gene or set of genes. A regulon is defined by the genes affected by it and the regulatory cofactors associated with it and can be different in various cell types or when studied from different perspectives. A given regulon may also be functional in more than one cell type. A Differon is the set of all genes that can be expressed in a specific cell and the differon defines the cell type. All the cells with the same differon are of the same type. (The differon differs from the transcriptome, the set of all mRNA expressed in a cell, because not all genes that can be expressed are always being expressed in a cell. For example, the liver may express certain genes only in response to the presence of specific toxins and so those genes will not appear in the transcriptome if the toxin is absent but those genes are still part of the differon)

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