The Developmental Organization of Regulatory States in the Sea Urchin Larva

Abstract

Development is an inherently dynamic process where cell fate specification occurs continuously and in a progressive manner. Thus, a major focus in developmental biology is solving the gene regulatory networks (GRNs) that underlie specification of cell fates. GRNs specify new spatial domains of cells by controlling the expression of their changing regulatory states throughout development. Regulatory states are composed of combinations of expressed regulatory genes which encode transcription factors that form regulatory circuits which function to carry out the specific developmental tasks involved in cell fate specification. To investigate the differences of GRNs operating in the embryo and their change over development, we sought to identify and characterize the regulatory states present in multiple developmental stages of sea urchin embryogenesis. We performed a genome-wide survey and embryo-wide annotation of regulatory gene expression by whole mount in situ hybridization at five consecutive developmental time-points in order to determine regulatory states and their developmental trajectory. We determined at least 74 distinct regulatory states expressed in discrete developmental domains which coincide with larval morphological structures and show that their progenitor domains foreshadow the ensuing larval morphology. Among these domains, we identified bilateral ciliary photoreceptors in the larva which express a distinct regulatory state that include factors known in ciliary photoreceptor specification. We show that this photoreceptor regulatory state does not express the genes of the retinal determination network that specify eyes in both flies and vertebrates. In addition, we show that though the sizes of regulatory states are comparable over developmental time, no two regulatory states are equal, even those expressed in a given domain at previous or subsequent developmental time-points. Lastly, we found that similarities among regulatory states reflect a common developmental function but not necessarily a common developmental history. The results suggest that the combinations of transcription factors defining regulatory states are both spatially and temporally dynamic in their progressive specification of cell fates during development and that regulatory state expression is tightly associated with the developing morphology of the larva.