Trapnell, ColeParichy, David MSaunders, Lauren Michelle2019-08-142019-08-142019-08-142019Saunders_washington_0250E_20070.pdfhttp://hdl.handle.net/1773/44402Thesis (Ph.D.)--University of Washington, 2019During the generation of adult form, circulating endocrine factors are important orchestrators of complex developmental processes. One such factor, thyroid hormone (TH), is essential for proper development and coordinates diverse, often contrasting, cellular events via mechanisms that are poorly understood. Pigmentation of adult zebrafish offers an unusually tractable model in which to address these issues as two neural crest-derived lineages -- black melanophores and yellow/orange xanthophores -- differ dramatically in their TH-dependence. I sought to define how TH elicits seemingly disparate outcomes in the abundance of these two pigment cell classes during pigment pattern formation. By profiling individual transcriptomes from thousands of neural crest-derived cells, including pigment cells, using single cell RNA-sequencing, I reconstructed developmental trajectories and identified lineage-specific responses to TH. Rather than acting on multipotent progenitors or directing specification towards one lineage or another, we find that TH promotes the maturation of both cell types in distinct ways. Additionally, to better understand how TH signaling differentially modulates gene expression programs in these lineages, I evaluated roles for TH nuclear receptors (TR), which classically repress gene expression in their unliganded form but activate target genes when ligand is present. By combining genetic analyses and thyroid ablation-induced hypothyroidism, we identify roles for TR-dependent repression during zebrafish post-embryonic development. Together, these studies provide insights into how TH defines and maintains diverse cell lineages during development and deepen our understanding of the neural crest-derived cell types that contribute to adult pigmentation in zebrafish. In this dissertation, I first introduce zebrafish pigment pattern formation as a model for studying diverse outcomes of global endocrine signaling during development. In Chapter 2, I detail our new understanding of how TH drives lineage-specific outcomes during pigment pattern formation. Specifically, we identify distinct roles for TH in the maturation of both melanophores and xanthophores. In melanophores TH drives a state of terminal differentiation and proliferative arrest, limiting the final number of these cells. In xanthophores, TH is required for the accumulation of yellow, carotenoid-based pigment as cells exit a cryptic phase. Moreover, I present findings that these maturation programs are gated by TRs. In a final chapter, I reflect on future directions for this work as well as promises and limitations of single-cell genomics for studying how global signals are translated into cell-type specific outcomes.application/pdfen-USnoneDevelopmentNeural CrestPigmentSingle Cell GenomicsThyroid HormoneZebrafishDevelopmental biologyGeneticsMolecular biologyMolecular and cellular biologyThesis