Gene Regulatory Network Analysis in Sea Urchin Embryos

Abstract

This chapter considers special methodologies developed for gene regulatory network (GRN) analysis and for the use of GRNs. The GRNs provide logic maps of the control functions that direct development, and they relate these maps directly to the genomic regulatory sequence. A GRN indicates what inputs into each regulatory gene are responsible for its spatial and temporal patterns of expression. It thereby explains the progression of regulatory states that underlies spatial specification of domain fate in development and thereafter the institution of regional cell differentiation. The chapter examines how intercellular signaling and developmentally important maternal anisotropies are linked into the gene regulatory apparatus of the embryonic cells—that is, why signaling interactions and localizations in the egg affect the developmental process. A properly constructed GRN has an immense predictive, as well as explanatory potentiality. The sea urchin embryo has turned out to be a material of choice for the system-level, high-throughput kinds of research required for GRN analysis. A large-scale provisional GRN for embryonic endomesoderm specification has been worked out for sea urchin (Strongylocentrotus purpuratus) embryos.