Most organizations is situated in other organizations. These relationships can be understood as nesting relationships.
One should always be very clear on which "level" one is talking about. One way to do this is to be explicit about the contained and containing levels.
strict digraph { rankdir=BT #layout=circo title="Three Level View" node [shape=box style=filled fillcolor=bisque] 1 [label="Bottom Level Orgs"] 2 [label="IN FOCUS\nMiddle Level Org"] 3 [label="Top Level Orgs"] 1->2 [label="makeup"] 2->3 [label="makeup"] 2->3 }