Transcriptome profiling of theCaenorhabditis elegansintestine reveals that ELT-2 negatively and positively regulates intestinal gene expression within the context of a gene regulatory network

Abstract

The transcription factor ELT-2 is the major factor required for Caenorhabditis elegans intestinal development. ELT-2 expression initiates in embryos, promoting development, but persists after hatching through larval and adult stages, where it contributes to diverse intestinal functions. How ELT-2's regulatory role changes over development is largely unexplored. We sought to determine whether ELT-2 target gene preference changes over developmental time and whether those changes underlie transcriptome dynamics. We analyzed stage-specific ELT-2 ChIP-seq assays to identify sets of dynamically changing ELT-2 peaks. Embryo-specific and larval-specific ELT-2 peaks were less common than peaks that accumulated in the L3 stage or progressively throughout development. To assess how ELT-2 occupancy related to transcriptional output, we compared patterns of ELT-2 occupancy over developmental time to intestinal expression dynamics and sets of ELT-2-dependent genes. ELT-2 occupancy predicted gene expression changes at larval but not embryonic stages, suggesting that ELT-2 promotes transcriptional output in some cases. However, we also found that ELT-2 negatively regulated a subset of its direct target genes. Repressed target genes were over-represented for neuronal and gonad functions, signifying that ELT-2 may protect the intestine from these tissue fates. Furthermore, we observed that ELT-2 repressed its own promoter in a negative feedback loop to stabilize elt-2 gene expression to a set amount. These findings illustrate that ELT-2 exerts both positive and negative regulatory control - turning on some target genes to promote intestinal function while down-regulating others to prevent or reduce their transcriptional output.

Hand Dissection of <em>Caenorhabditis elegans</em> Intestines

“…Our lab routinely utilizes FACS to purify intestinal cells post isolation 30 , post-hoc analysis methods for intestinal cell identification, and this hand dissection method 30 , 42 . Hand dissection has the advantage of being amenable for use in adult worms when worm disaggregation and cell isolation are less successful.…”

“…Each approach has its advantages and limitations. For the C. elegans intestine, worm disaggregation and FACS isolation of intestinal cells is achievable in the embryo and larval stages 30 but is challenging in adults. This is thought to be due to the intestine's large, endoreduplicated, and strongly adherent cells making them difficult to dissociate undamaged.…”