A novel paired domain DNA recognition motif can mediate Pax2 repression ofgene transcription

The paired domain (PD) is an evolutionarily conserved DNA-binding domain en coded by the Pax gene family of developmental regulators. The Pax proteins are transcription factors and are involved in a variety of processes such a s brain development, patterning of the central nervous system (CNS), and B- cell development. In this report we demonstrate that the zebrafish Pax2 PD can interact with a novel type of DNA sequences in vitro, the triple-a moti f, consisting of a heptameric nucleotide sequence G/CAAACA/TC with an invar iant core of three adjacent adenosines. This recognition sequence was found to be conserved in known natural Pax5 repressor elements involved in contr olling the expression of the p53 and J-chain genes. By identifying similar high affinity binding sites in potential target genes of the Pax2 protein, including the pax2 gene itself, we obtained further evidence that the tripl e-A sites are biologically significant. The putative natural target sites a lso provide a basis for defining an extended consensus recognition sequence . In addition, we observed in transformation assays a direct correlation be tween Pax2 repressor activity and the presence of triple-A sites. The resul ts suggest that a transcriptional regulatory function of Pax proteins can b e modulated by PD binding to different categories of target sequences. (C) 1999 Academic Press.