Old questions and new insights: a comparison of development and regeneration in the acoel worm Hofstenia Miamia

Abstract

Development and regeneration both result in the formation of a complete adult body plan. Although these processes have different starting points – from the single-celled zygote during development versus from the many differentiated cell types present in a regenerating adult animal – they share many key processes, e.g.,the establishment of major body axes and the differentiation of cellular lineages. These similarities have led to longstanding questions regarding the relationship between the two processes, and the hypothesis that regeneration could include redeployment of developmental mechanisms. This raises the question of how developmental pathways are re-accessed during regeneration, which further has implications for understanding the evolution of regeneration, and why regeneration may succeed or fail in different taxa. In past studies, reuse of developmental genes during regeneration has been demonstrated in multiple species by both broad and specific process comparisons. However, given their distinct starting points, the mechanisms allowing for the re-use of developmental processes during regeneration are active areas of investigation. In this dissertation I used the highly regenerative acoel worm Hofstenia miamia to conduct both broad and targeted investigations comparing development and regeneration. In Chapter 2, I produced a developmental ATAC-seq dataset that is needed to assess regulatory mechanisms during development relative to regeneration. Using these data, I investigated the regulatory landscape of H.miamia embryogenesis, characterizing large scale changes in chromatin accessibility and putative regulators of tissue identity. In Chapter 3, I undertook a thorough investigation of development and regeneration in H.miamia. I compared transcriptome-wide gene expression, and similar to other species found high overlap between gene use in development and regeneration. However, the temporal order regarding when these genes were expressed relative to one another was different in the two processes, consistent with other studies indicating that regeneration is not a strict recapitulation of development. Targeted comparisons of key components shared between regeneration and development, including cell specification and re-establishment of posterior patterning, showed similarities in pathway progression and also revealed development and regeneration-specific features, especially in the expression of early pathway components. We further found that the network architecture of a wound-response program was likely a regeneration-specific innovation. Chromatin accessibility analyses suggested that similar regulatory regions control expression of shared genes in development and regeneration, regardless of similar or distinct expression patterns, likely via distinct transcription factor binding sites. This was even true of wound-induce genes, which have been postulated in other systems to be controlled by distinct regulatory elements. These findings provide new resolution as to how developmental processes could be reactivated in response to wounding. Furthermore, this study represents the first such comparison of development and regeneration in Xenacoelmorpha, an enigmatic phylum placed either as sister to Ambulacraria or to other bilaterians. The tools I utilized to conduct these investigations are applicable to new research organisms, opening the door to similar comparisons in an even broader range of organisms.