the behavior shown here was computed for one particular set of parameter values describing the quantitative properties of A, B, and the product of Z, along with their syntheses. with different values of these parameters, feed-forward loops can in principle perform other types of “calculations.” Many feed-forward loops have been discovered in cells, and theoretical analysis helps researchers to discern—and subsequently test—the different ways in which they may function (see figure 8–86). (Adapted from
S.S. Shen-Orr et al., Nat. Genet. 31:64–68, 2002. with permission from Macmillan publishers ltd.)
Figure 7–42 The exceedingly complex gene circuit that specifies a portion of the developing sea urchin embryo. each colored small box represents a different gene. those in yellow code for transcription regulators and those in green and blue code for proteins that give cells of the mesoderm and endoderm, respectively, their specialized characteristics. Genes depicted in gray are largely active in the mother and provide the egg with cues needed for proper development. As in figure 7–40, arrows depict instances in which a transcription regulator activates the transcription of another gene. lines ending in bars indicate examples of gene repression. (from i.S. peter and  e.h. Davidson, Nature 474:635–639, 2011. with permission from Macmillan  publishers ltd.)
The many types of cells in animals and plants are created largely through mechanisms that cause different sets of genes to be transcribed in different cells. The transcription of any particular gene is generally controlled by a combination of transcription regulators. Each type of cell in a higher eukaryotic organism contains a specific set of transcription regulators that ensures the expression of only those genes appropriate to that type of cell. A given transcription regulator may be active in a variety of circumstances and is typically involved in the regulation of many different genes.
Since specialized animal cells can maintain their unique character through many cell-division cycles, and even when grown in culture, the gene regulatory mechanisms involved in creating them must be stable once established and heritable when the cell divides. These features reflect the cell’s memory of its developmental history. Direct or indirect positive feedback loops, which enable transcription regulators to perpetuate their own synthesis, provide the simplest mechanism for cell memory. Transcription circuits also provide the cell with the means to carry out other types of logic operations. Simple transcription circuits combined into large regulatory networks drive highly sophisticated programs of embryonic development that will require new approaches to decipher.
Thus far in this chapter, we have emphasized the regulation of gene transcription by proteins that associate either directly or indirectly with DNA. However, DNA itself can be covalently modified, and certain types of chromatin states appear to be inherited. In this section, we shall see how these phenomena also provide opportunities for the regulation of gene expression. At the end of this section, we discuss how, in mice and humans, an entire chromosome can be transcription-ally inactivated using such mechanisms, and how this state can be maintained through many cell divisions.
patterns of DnA Methylation Can Be inherited when vertebrate Cells Divide