I have been characterizing a potential cis-element within a gene promoter by Dual-luciferase reporter system. To my surprise, I found two identical DNA regions(about 10bp) flanking the studied element(at a distance of 100bp)could reverse the studied element activity. The effect was confirmed by comprehensive mutation. So is there anyone who is knowledged about this strange phenomemon?
Something very similar is mentioned in this paper (except for the distance between regulatory elements), maybe it could be useful for your own model: http://atvb.ahajournals.org/content/19/11/2591.full
Maybe it is not exactly what you are looking for, but if you check from my publications (Functional analysis of the Arabidopsis PLDZ2 promoter
reveals an evolutionarily conserved low-Pi-responsive
transcriptional enhancer element), we identified a regulatory region containing two nearly identical motifs, both of them necessary for the function of the enhancer element. When the region between them was mutated, the enhancer function was affected, implying the presence of at least a third element. Sequence analysis of homologous promoters does indeed show a conserved element in that spacer region. We have not performed specific mutations to find out if that element is the one directly affecting the enhancer function, though.
Anyway, these examples show that combinatorial regulation is quite common in animals and plants, and you can find a lot of distinct arrangements of cis-elements that can lead to a very particular expression pattern.
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