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Ancestral state reconstruction by comparative analysis of a GRN kernel operating in echinoderms
Citation: Erkenbrack, E. M., Ako-Asare, K., Miller, E., Tekelenburg, S., Thompson, J. R., & Romano, L. (2016). Ancestral state reconstruction by comparative analysis of a GRN kernel operating in echinoderms. Development Genes and Evolution, 226(1), 37-45.
Diverse sampling of organisms across the five ma- jor classes in the phylum Echinodermata is beginning to reveal much about the structure and function of gene regulatory net- works (GRNs) in development and evolution. Sea urchins are the most studied clade within this phylum, and recent work suggests there has been dramatic rewiring at the top of the skeletogenic GRN along the lineage leading to extant mem- bers of the euechinoid sea urchins. Such rewiring likely ac- counts for some of the observed developmental differences between the two major subclasses of sea urchins—cidaroids and euechinoids. To address effects of topmost rewiring on downstream GRN events, we cloned four downstream regu- latory genes within the skeletogenic GRN and surveyed their spatiotemporal expression patterns in the cidaroid Eucidaris tribuloides. We performed phylogenetic analyses with homo- logs from other non-vertebrate deuterostomes and character- ized their spatiotemporal expression by quantitative polymer- ase chain reaction (qPCR) and whole-mount in situ hybridi- zation (WMISH). Our data suggest the erg–hex–tgif subcircuit, a putative GRN kernel, exhibits a mesoderm- specific expression pattern early in Eucidaris development that is directly downstream of the initial mesodermal GRN circuitry. Comparative analysis of the expression of this subcircuit in four echinoderm taxa allowed robust ancestral state reconstruction, supporting hypotheses that its ancestral function was to stabilize the mesodermal regulatory state and that it has been co-opted and deployed as a unit in mesodermal subdomains in distantly diverged echinoderms. Importantly, our study supports the notion that GRN kernels exhibit struc- tural and functional modularity, locking down and stabilizing clade-specific, embryonic regulatory states.

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