A model for the temporal control of pharyngeal gene expression as proposed by Gaudet et al. . The temporal expression patterns of four transcription factors are shown at the top, and the promoters of four genes (A-D) that are expressed at different times during pharyngeal development are shown below. EARLY1, LATE1 and LATE2 are the putative transcription factors assumed to bind to the promoter elements Early-1, Late-1 and Late-2 identified by Gaudet et al.  and shown in Figure 1; the factors themselves have not been identified. Varying combinations of PHA-4-binding sites and temporal cis-regulatory elements drive expression of genes A-D at different times during pharyngeal development. In this model neither the PHA-4-binding site nor any of the temporal elements alone is sufficient for gene activation. Early expression of gene A is driven by recruitment of PHA-4 (black circle) to a high-affinity site (black box) along with recruitment of the putative EARLY1 factor (white circle) to an Early-1 site (white box). As PHA-4 is present at low levels early in development, only a gene carrying a high-affinity PHA-4 site can efficiently recruit PHA-4 for activation. As PHA-4 levels increase over the course of development, however, genes such as C that carry a low-affinity PHA-4 site (hatched black and white boxes) can also be activated. The onset of expression of gene C is primarily controlled by the affinity of PHA-4 for its site rather than by the Early-1 site or the EARLY1 factor, which may be expressed at stable levels throughout development. Expression of gene B is derepressed when the putative repressor LATE1 (light gray hexagon) falls to low enough levels to vacate the Late-1 site (light gray box). The timing of expression of a gene carrying a Late-1 site could be further retarded if the Late-1 site was paired with a low-affinity PHA-4-binding site. Transcription of gene D is activated late in development when the putative factor LATE2 (dark gray circle) rises to high enough levels to be recruited to the Late-2 site (dark gray box). The timing of expression of gene D could be advanced by pairing the Late-2 site with a high-affinity PHA-4-binding site.
Banerjee and Slack Genome Biology 2005 6:205 doi:10.1186/gb-2005-6-2-205