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Encoding regulatory state boundaries in the pregastrular oral ectoderm of the sea urchin embryo

Significance Regulatory state boundary formation is a general process in early development, in which embryonic territory is divided up into spatial domains that express distinct sets of regulatory genes. We establish the mechanistic principles by which multiple orthogonal boundaries of this kind are progressively formed on the oral side of the sea urchin embryo, according to an encoded genomic program. These boundaries separate prospective endoderm from ectoderm domains, neurogenic from non-neurogenic domains, and ciliated band from oral ectoderm domains and produce an orthogonal grid of regulatory states. Boundary formation invariably depends on spatial transcriptional repression superimposed on more widespread domains of transcriptional activation. By gastrulation the ectodermal territories of the sea urchin embryo have developed an unexpectedly complex spatial pattern of sharply bounded regulatory states, organized orthogonally with respect to the animal/vegetal and oral/aboral axes of the embryo. Although much is known of the gene regulatory network (GRN) linkages that generate these regulatory states, the principles by which the boundaries between them are positioned and maintained have remained undiscovered. Here we determine the encoded genomic logic responsible for the boundaries of the oral aspect of the embryo that separate endoderm from ectoderm and ectoderm from neurogenic apical plate and that delineate the several further subdivisions into which the oral ectoderm per se is partitioned. Comprehensive regulatory state maps, including all spatially expressed oral ectoderm regulatory genes, were established. The circuitry at each boundary deploys specific repressors of regulatory states across the boundary, identified in this work, plus activation by broadly expressed positive regulators. These network linkages are integrated with previously established interactions on the oral/aboral axis to generate a GRN model encompassing the 2D organization of the regulatory state pattern in the pregastrular oral ectoderm of the embryo.