AN ATYPICAL HOMEODOMAIN IN SATB1 PROMOTES SPECIFIC RECOGNITION OF THEKEY STRUCTURAL ELEMENT IN A MATRIX ATTACHMENT REGION

SATB1 is a cell type-specific nuclear matrix attachment region (MAR) D NA-binding protein, predominantly expressed in thymocytes. We identifi ed an atyp ical homeodomain and two Cut like repeats in SATB1, in addi tion to the known MAR-binding domain. The isolated MAR-binding domain recognizes a certain DNA sequence context within MARs that is highly p otentiated for base unpairing. Unlike the MAR-binding domain, the home odomain when isolated binds poorly and with low specificity to DNA. Ho wever, the combined action of the MAR-binding domain and the homeodoma in allows SATB1 to specifically recognize the core unwinding element w ithin the base-unpairing region. The core unwinding element is critica l for MAR structure, since point mutations within this core abolish th e unwinding propensity of the MAR. The contribution of the homeodomain is abolished by alanine substitutions of arginine 3 and arginine 5 in the N-terminal arm of the homeodomain. Site-directed mutagenesis of t he core unwinding element in the 3' MAR of the immunoglobulin heavy ch ain gene enhancer revealed the sequence 5'-(C/A)TAATA-3' to be essenti al for the increase in affinity mediated by the homeodomain. SATB1 may regulate T-cell development and function at the level of higher order chromatin structure through the critical DNA structural elements with in MARs.