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Prox1 dynamically regulates downstream targets and chromatin accessibility during venous to lymphatic endothelial cell transdifferentiation in the embryo

During development, lymphatic vasculature forms as a second, distinct vascular network derived from blood vessels. Transdifferentiation of venous into lymphatic endothelial cells (LECs) is the first step in this process. Specification, transdifferentiation and maintenance of LEC fate requires the transcription factor Prox1 but downstream mechanisms and markers remain to be described in full. We present a single cell transcriptomic atlas of lymphangiogenesis in zebrafish revealing new markers and hallmarks of LEC differentiation. We further profile single cell transcriptomic and chromatin accessibility changes in Prox1 mutants. This work reveals dynamic, multifaceted roles for Prox1 that include blocking blood vascular and hematopoietic fate and up-regulating essential factors for lymphatic development. We reveal that Prox1 controls chromatin state and evidence for Prox1-independent regulation of early LEC differentiation. This work thus provides new insights and a detailed resource for further understanding an enigmatic developmental process that is central in pathological lymphangiogenesis in disease.