A critical question in developmental biology is how complex programs of gene expression are orchestrated by a class of regulators known as selector genes. Selector genes code for transcription factors that autonomously govern the fates of groups of cells related to each other by virtue of their cell type, position or affiliation to an organ1. For example, the FoxA transcription factor PHA-4 dictates the identity of cells within the C. elegans pharynx. Embryos that lack
pha-4 fail to generate pharyngeal cells, and these cells acquire an alternative ectodermal fate instead2,3. Our lab has previously demonstrated that PHA-4 can modulate the temporal expression of pharyngeal target genes through the affinity of PHA-4 to its binding site4, and cooperative binding of cis-regulatory elements5,6. Here we further refine our model by showing that PHA-4 cooperates with a chromatin remodeling complex to execute the proper timing of pharyngeally expressed genes.
Our data have revealed that
pha-4 synergizes with components of the histone modifying/remodeling complex known as Esa1-Swr1 in yeast, or SCRAP in Humans7, to promote activation of pharyngeal gene expression during organogenesis. Partial inactivation of
pha-4 in combination with
htz-1/H2A.Z,
mys-1/TIP60, or
ssl-1/Swr1 RNAi resulted in a specific synergistic lethality that is not observed with other transcription factors. A nuclear spot assay was used to visualize HTZ-1 binding to pharyngeal targets in living embryos (e.g.
myo-2, R07B1.9 promoters). Pharyngeal promoters preferentially associated with HTZ-1 in pharyngeal cells, and this association depended upon PHA-4. HTZ-1 was transiently recruited to the
myo-2 promoter at initiation of expression, and
htz-1(RNAi) delayed the onset of
myo-2 expression, but only in the presence of PHA-4 binding sites. We suggest that PHA-4 and HTZ-1 coordinate temporal gene expression by modulating the chromatin environment.