Figure 1.

SeqChIP experiments have three different outcomes: complete co-occupancy, no co-occupancy, and partial co-occupancy. In full co-occupancy, proteins A and B always co-occupy promoters; neither one is found bound to a particular region without the other. No co-occupancy occurs when DNA binding of A and B is mutually exclusive. Partial co-occupancy has two distinct states: in the first, the binding of B is critically dependent on binding of A, but not vice versa. In the second state, both A and B can bind DNA independently, but may or may not be simultaneously bound on the same DNA fragments.