Project 2: Genome-wide identification of regeneration enhancers


The Damage-Activated Regeneration Enhancer of the WNT genes (DAREWNT) is the principal example of such a regulatory region, directing regenerative gene expression and controlling their ability to be activated over developmental time. However, we know of many genes that are similarly activated by damage in younger tissues, but not in older. We hypothesize that the mechanism that regulates the WNT genes would be a powerful yet simple way to simultaneously regulate the many genes that comprise a regeneration program, and hence direct the regenerative response on a tissue-wide scale.  Consistent with this hypothesis, we have identified another DARE that regulates the MMP1 gene in the context of regeneration, and are currently exploring this example. Building on these examples, we are using whole genome sequencing approaches to perform epigenetic landscape analysis and transcriptional profiling to identify and characterize potential DAREs genome-wide:


  • What candidate genes are regulated by this regeneration enhancer mechanism? We have identified two examples of such a bipartite regulatory region (DAREWNT and DAREMMP1) that pertain to regenerative gene expression. Do they have elements in common that could tell us more about how this regulatory mechanism functions?
  • What other unidentified regeneration genes are regulated by this enhancer mechanism? We have used ATAC-seq and RNA-seq to identify changes in the epigenetic landscape and coincident changes in gene expression in tissues that can regenerate (young discs) and those that can’t (old discs). This analysis has revealed many hundreds of target genes that are differentially expressed in regenerating tissue vs. undamaged and, importantly, that change in their ability to be activated in response to damage in older discs vs younger. Thus these changes are coincident with, and possibly responsible for, the loss of regenerative capacity of a developing tissue.