Temporal and spatial patterning of an organ by a single transcription factor

Abstract

During the formation of animal organs, a single regulatory factor can control the majority of cell-fate decisions, but the mechanisms by which this occurs are poorly understood. One such regulator, the nematode transcription factor PHA-4, functions together with various cis-regulatory elements in target genes to regulate spatial and temporal patterning during development of the pharynx.

Figure 1

An outline of the experimental strategy used by Mango and colleagues [8,9] to identify regulatory motifs that specify temporal and spatial patterns of gene expression during pharyngeal development. (a) RNA was isolated from worms with mutations in the par-1 or skn-1 genes, which have excess or no pharyngeal cells, respectively. (b) The RNA from the two strains was compared using a whole-genome microarray. (c) Transcripts with high levels of expression in par-1 worms compared with skn-1 worms were selected and sorted into groups according to their temporal [9] or spatial [8] pattern of expression. For the temporal groupings the genes were divided into those expressed early or late in pharynx development; for the spatial groupings they were divided into those expressed in the muscles, glands, pharyngeal marginal cells or epithelium, plus those that were expressed in both the muscles and the marginal cells. (d) The promoters of the genes in each group were analyzed using the Improbizer algorithm to find sequence elements that were significantly enriched in each group; these were named Early-1, M2, and so on. A selection of these is shown.

Figure 2

A model for the temporal control of pharyngeal gene expression as proposed by Gaudet et al. [9]. 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. [9] 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.