Cis-regulatory logic in the endo16 gene: switching from a specification toa differentiation mode of control

The endo16 gene of Strongylocentrotus purpuratus encodes a secreted protein of the embryonic and larval midgut, The overall functional organization of the spatial and temporal control system of this gene are relatively well k nown from a series of earlier cia-regulatory studies. Our recent computatio nal model for the logic operations of the proximal region of the endo16 con trol system (Module A) specifies the function of interactions at each trans cription factor target site of Module A. Here, we extend sequence level fun ctional analysis to the adjacent cia-regulatory region, Module B, The compu tational logic model is broadened to include B/A interactions as well as ot her Module B functions, Module B drives expression later in development and its major activator is responsible for a sharp, gut-specific increase in t ranscription after gastrulation, As shown earlier, Module B output undergoe s a synergistic amplification that requires interactions within Module A, T he interactions within Module B that are required to generate and transmit its output to Module A are identified. Logic considerations predicted an in ternal cis-regulatory switch by which spatial control of endo16 expression is shifted from Module A (early) to Module B (later), This prediction was c onfirmed experimentally and a distinct set of interactions in Module B that mediate the switch function was demonstrated. The endo16 computational mod el now provides a detailed explanation of the information processing functi ons executed by the cis-regulatory system of this gene throughout embryogen esis. Early in development the gene participates in the specification event s that define the endomesoderm; later it functions as a gut-specific differ entiation gene, The cis-regulatory switch mediates this functional change.