Chromatin Regulation of Tissue Regeneration and Stem Cell Function

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Regeneration is a remarkable phenomenon that is both ubiquitous and mysterious; although many different animals are capable of replacing damaged and/or lost structures, it is unclear how these regenerative species maintain both the cellular stability required for tissue integrity and the cellular plasticity needed to reactivate tissue development upon injury. Moreover, as regeneration is often induced by spontaneous and imprecise tissue damage, how do cells translate broad and sudden signals into cell-type-specific transcriptional changes? Genomic regulators such as transcription factors and chromatin-modifying enzymes work together to instruct cell fate during developmental processes. Although there is substantial data describing how these factors orchestrate embryogenesis, much less is known about how they are activated to induce regeneration. My central hypothesis is that chromatin serves as a mediator between the signaling events that are triggered by significant tissue loss and the cellular changes they induce to activate regeneration. To uncover the fundamental molecular mechanisms underlying this process, my laboratory studies the planarian model of animal regeneration. Planarians are free-living flatworms with incredible regenerative capacities. They are also amenable to genetic perturbation through RNAi, easily dissociated for single cell analyses, and encode chromatin modifying proteins with strong homology to those in other organisms. We are particularly interested in how some planarian cell types respond to injury by activating specific, essential, regeneration genes, while others activate an entirely different set of loci in response to the same injury. My lab uses multiple customized methods to isolate specific planarian cell types, both differentiated and stem cells, in order to characterize the chromatin state of these cell types before and after injury. We also leverage data showing that RNAi depletion of the MLL1/2 chromatin enzyme in the planarian Schmidtea mediterranea leads to loss of cilia on its outer epithelium. In addition, we have recently isolated and characterized a new planarian species that has a unique cilia pattern on its outer epithelium, providing an exciting opportunity to use comparative genomic approaches to identify specific genes that are linked to this particular trait. Combining all these approaches, we aim to dissect the functional role and molecular signaling cues contributed by specific cell types during regeneration. The outer epithelium and other differentiated tissues are essential for planarian regeneration in large part because they signal to a population of heterogeneous multi and pluripotent stem cells that are maintained in adult planarians. Because these stem cells must differentiate into all needed cell types in response to missing tissue signals, it is not surprising that they are highly plastic and transcriptionally heterogeneous. Yet it is unknown how they create and maintain this heterogeneity in vivo. We will test the hypothesis that a conserved chromatin signature regulates this critical feature. These studies will uncover important mechanisms underlying both regeneration and other biological processes that require dynamic gene regulation across complex tissues.