Whole-Genome Analysis of Temporal Gene Expression during Foregut Development

Abstract

We have investigated the cis-regulatory network that mediates temporal gene expression during organogenesis. Previous studies demonstrated that the organ selector gene pha-4/FoxA is critical to establish the onset of transcription of Caenorhabditis elegans foregut (pharynx) genes. Here, we discover additional cis-regulatory elements that function in combination with PHA-4. We use a computational approach to identify candidate cis-regulatory sites for genes activated either early or late during pharyngeal development. Analysis of natural or synthetic promoters reveals that six of these sites function in vivo. The newly discovered temporal elements, together with predicted PHA-4 sites, account for the onset of expression of roughly half of the pharyngeal genes examined. Moreover, combinations of temporal elements and PHA-4 sites can be used in genome-wide searches to predict pharyngeal genes, with more than 85% accuracy for their onset of expression. These findings suggest a regulatory code for temporal gene expression during foregut development and provide a means to predict gene expression patterns based solely on genomic sequence.

Automated cell lineage tracing in Caenorhabditis elegans

“…Microarray and serial analysis of gene expression data combined with homeotic mutants (12,13), RNA enrichment methods (14), or FACS sorting of individual cells (15) reveal active genes within particular cells or stages of development. In situ hybridization (16) can localize mRNAs to particular stages and tissues.…”

Genetic Suppressors ofCaenorhabditis elegans pha-4/FoxAIdentify the Predicted AAA Helicaseruvb-1/RuvB

“…First stage larvae do not express PHA-4TGFP in their gonads (data not shown), and L1 animals with pha-4(null) mutations are born with a normal gonad primordium (Mango et al 1994). However, we observed that as larval development progressed, PHA-4TGFP (Alder et al 2003) was activated in the developing gonad ( Figure 4A; Kalb et al 1998;Gaudet et al 2004) and was required for its proper formation ( Figure 4B; Ao et al 2004). A shift of pha-4(ts) larvae to nonpermissive temperature (20°) at the L1 stage produced sterile adults ( Figure 4B).…”

“…The targets are expressed at varying times during the development, differentiation, or functioning of the pharynx. The appropriate timing of expression depends on combinatorial mechanisms among different cis-regulatory sites (Kalb et al 2002;Ao et al 2004;Gaudet et al 2004;Vilimas et al 2004;Raharjo and Gaudet 2007). In addition, the affinity of PHA-4 for its binding sites is an important contributor to temporal control (Gaudet and Mango 2002;Ao et al 2004;Gaudet et al 2004).…”

“…The appropriate timing of expression depends on combinatorial mechanisms among different cis-regulatory sites (Kalb et al 2002;Ao et al 2004;Gaudet et al 2004;Vilimas et al 2004;Raharjo and Gaudet 2007). In addition, the affinity of PHA-4 for its binding sites is an important contributor to temporal control (Gaudet and Mango 2002;Ao et al 2004;Gaudet et al 2004). FoxA proteins recognize the consensus TRTTKRY (R ¼ A/G, K ¼ T/G, and Y ¼ T/C) in the cis-regulatory regions of gut-specific targets (Overdier et al 1994;Kalb et al 1998;Gaudet and Mango 2002).…”

“…FoxA proteins recognize the consensus TRTTKRY (R ¼ A/G, K ¼ T/G, and Y ¼ T/C) in the cis-regulatory regions of gut-specific targets (Overdier et al 1994;Kalb et al 1998;Gaudet and Mango 2002). Target genes with high affinity sites are competent to fire early in embryogenesis, whereas genes with lower affinity sites are typically expressed late (Gaudet and Mango 2002;Gaudet et al 2004). This regulatory configuration implies that the level and activity of PHA-4 are carefully controlled to achieve proper timing for pharyngeally expressed genes.…”