title: A novel Pax-6 binding site in rodent B1 repetitive elements: coevolution between developmental regulation and repeated elements?
abstract: 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 15bp region (hGCalpha1BLs5) that is sufficient for PAX6 specific binding. From a homology search in the GenBank, we found that an hGCalpha1BLs5-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 hGCalpha1BLs5 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.
authors.affiliation: Department of Biochemistry, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA. sa51001@odin.mdacc.tmc.edu
authors.forename: Y
authors.initials: Y
authors.lastname: Zhou
authors.forename: J B
authors.initials: JB
authors.lastname: Zheng
authors.forename: X
authors.initials: X
authors.lastname: Gu
authors.forename: W
authors.initials: W
authors.lastname: Li
authors.forename: G F
authors.initials: GF
authors.lastname: Saunders
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D001667:Binding, Competitive; D004247:DNA / Q000737:chemistry / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D019143:Evolution, Molecular; D005136:Eye Proteins; D018507:Gene Expression Regulation, Developmental; D018398:Homeodomain Proteins; D006801:Humans; D020014:K562 Cells; D051379:Mice; D008969:Molecular Sequence Data; D009154:Mutation; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000378:metabolism; D000071841:PAX6 Transcription Factor; D051761:Paired Box Transcription Factors; D010802:Phylogeny; D011485:Protein Binding; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D012097:Repressor Proteins; D012377:Rodentia; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid
chemical_list: D004268:DNA-Binding Proteins; D005136:Eye Proteins; D018398:Homeodomain Proteins; D009841:Oligonucleotides; D000071841:PAX6 Transcription Factor; C000605730:PAX6 protein, human; D051761:Paired Box Transcription Factors; C000605732:Pax6 protein, mouse; D012097:Repressor Proteins; D004247:DNA