A novel Pax-6 binding site in rodent B1 repetitive elements: coevolution between developmental regulation and repeated elements?

Pax-6 encodes a transcription factor that is important in the development o f eye and CNS. Identification of Pax-6 target genes is crucial for understa nding the gene regulatory network in these developmental processes. Using a n in-vitro approach of cyclic amplification of the protein binding sequence s (CAPBS), we isolated a PAX6 binding sequence from a human single-copy (sc ) DNA library. Characterization of this PAX6 binding sequence revealed a 15 bp region (hGC alpha 1BLs5) that is sufficient for PAX6 specific binding. From a homology search in the GenBank, we found that an hGC alpha 1BLs5-lik e Pax-6 binding site exists in 21 genes (16 from rodent), 15 of which were shown to be able to bind Pax-6 in vitro. Interestingly, some of these sites occur in B1 repetitive elements. Although hGC alpha 1BLs5 is highly simila r to a region in B1 repetitive elements, PAX6 does not bind to the consensu s sequence in B1. However, a single-step mutation in some B1 elements can l ead to a gain of function for PAX6 binding. This experimental evidence and phylogenetic analysis raise an interesting speculation for the coevolution between PAX6 regulation and repeat elements. Since a (Pax-6-binding) null B 1 element can be re-activated by even a single-step mutation, it has the po tential to recruit gene targets for Pax-6 if it is inserted into the regula tory region, and therefore may play a role for evolutionary modification of Pax-6 regulation. (C) 2000 Elsevier Science B.V. All rights reserved.