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

• Published in: Gene 2000-03, Vol.245 (2), p.319-328
• Main Authors: Zhou, Yi-Hong, Zheng, Jessica B., Gu, Xun, Li, Wen-Hsuing, Saunders, Grady F.
• Format: Article
• Language: English
• Subjects: Animals; B1 repetitive elements; Base Sequence; Binding Sites - genetics; Binding, Competitive; DNA - chemistry; DNA - genetics; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Electrophoresis, Polyacrylamide Gel; Evolution, Molecular; Evolutionary mechanisms; Eye Proteins; Gene Expression Regulation, Developmental; Gene recruitment; Homeodomain Proteins; Humans; K562 Cells; Mice; Molecular Sequence Data; Mutation; Oligonucleotides - chemical synthesis; Oligonucleotides - metabolism; Paired Box Transcription Factors; Pax-6 protein; PAX6 binding site; PAX6 Transcription Factor; Phylogeny; Protein Binding; Repetitive Sequences, Nucleic Acid - genetics; Repressor Proteins; Rodentia; Sequence Analysis, DNA; Sequence Homology, Nucleic Acid
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/S0378-1119(00)00019-6

Pax-6 encodes a transcription factor that is important in the development of eye and CNS. Identification of Pax-6 target genes is crucial for understanding the gene regulatory network in these developmental processes. Using an in-vitro approach of cyclic amplification of the protein binding sequences (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 (hGCα1BLs5) that is sufficient for PAX6 specific binding. From a homology search in the GenBank, we found that an hGCα1BLs5-like 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 hGCα1BLs5 is highly similar to a region in B1 repetitive elements, PAX6 does not bind to the consensus sequence in B1. However, a single-step mutation in some B1 elements can lead 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 B1 element can be re-activated by even a single-step mutation, it has the potential to recruit gene targets for Pax-6 if it is inserted into the regulatory region, and therefore may play a role for evolutionary modification of Pax-6 regulation.