A NOVEL DNA-BINDING MOTIF IN THE NUCLEAR MATRIX ATTACHMENT DNA-BINDING PROTEIN SATB1

The nuclear matrix attachment DNA (MAR) binding protein SATB1 is a seq uence context-specific binding protein that binds in the minor groove, making virtually no contact with the DNA bases, The SATB1 binding sit es consist of a special AT-rich sequence context in,which one strand i s well-mixed A's, T's, and C's, excluding G's (ATC sequences), which i s typically found in clusters within different MARs. To determine the extent of conservation of the SATB1 gene among different species, we c loned a mouse homolog of the human SATB1 cDNA from a cDNA expression l ibrary of the mouse thymus, the tissue in which this protein is predom inantly expressed. This mouse cDNA encodes a 764-amino-acid protein,vi th a 98% homology in amino acid sequence to the human SATB1 originally cloned from testis. To characterize the DNA binding domain of this no vel class of protein, we used the mouse SATB1 cDNA and delineated a 15 0-amino-acid polypeptide as the binding domain, This region confers fu ll DNA binding activity, recognizes the specific sequence context, and makes direct contact with DNA at the same nucleotides as the whole pr otein. This DNA binding domain contains a novel DNA binding motif: whe n no more than 21 amino acids at either the N- or C-terminal end of th e binding domain are deleted, the majority of the DNA binding activity is lost. The concomitant presence of both terminal sequences is manda tory for binding. These two terminal regions consist of hydrophilic am ino acids and share homologous sequences that are different from those of any known DNA binding motifs. We propose that the DNA binding regi on of SATB1 extends its two terminal regions toward DNA to make direct contact with DNA.