One of the most important questions in regenerative biology is how and when genes change expression to trigger regeneration programs. Resetting of gene expression patterns during injury responses is shaped by the coordinated action of genomic regions that integrate the activity of multiple sequence-specific DNA binding proteins. Using genome-wide approaches to interrogate chromatin function we identify the regulatory elements governing tissue recovery in Drosophila imaginal discs, which show a high regenerative capacity after genetically induced cell death. Our findings indicate a global co-regulation of gene expression as well as the existence of a regeneration program driven by different types of regulatory elements. Novel enhancers acting exclusively in the damaged tissue cooperate with enhancers co-opted from other tissues and developmental stages, and with endogenous enhancers that show increased activity after injury. These enhancers host binding sites for regulatory proteins, including a core set of conserved transcription factors that regulate regeneration across metazoans.
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