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Abstract
SATB1 is a cell type-specific nuclear matrix attachment region (MAR) DNA-binding protein, predominantly expressed in thymocytes. We identified an atypical homeodomain and two Cut-like repeats in SATB1, in addition to the known MAR-binding domain. The isolated MAR-binding domain recognizes a certain DNA sequence context within MARs that is highly potentiated for base unpairing. Unlike the MAR-binding domain, the homeodomain when isolated binds poorly and with low specificity to DNA. However, the combined action of the MAR-binding domain and the homeodomain allows SATB1 to specifically recognize the core unwinding element within the base-unpairing region. The core unwinding element is critical for MAR structure, since point mutations within this core abolish the 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 the core unwinding element in the 3' MAR of the immunoglobulin heavy chain gene enhancer revealed the sequence 5'-(C/A)TAATA-3' to be essential 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 within MARs.
Highlights
§ Present address: Dept. of Immunology, The Scripps Research Institute, 10550 N
These proteins bind with high affinity to matrix attachment region (MAR), and we showed that nucleolin and p114 can distinguish wild-type [25]5 from mutated [24]8
Repeat A occurs at the center of the MAR-binding domain of SATB1, but it does not include the Nand C-terminal amino acids that are mandatory for MAR binding [20]
Summary
§ Present address: Dept. of Immunology, The Scripps Research Institute, 10550 N. SATB1 defines a novel class of DNA-binding proteins that recognize a specific sequence context that exhibits a high base unpairing or unwinding propensity. When associated with the MAR-binding domain, the SATB1 homeodomain enhances binding specificity toward the core unwinding element of a MAR.
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