THE GENOMIC SEQUENCES BOUND TO SPECIAL AT-RICH SEQUENCE-BINDING PROTEIN-1 (SATB1) IN-VIVO IN JURKAT T-CELLS ARE TIGHTLY ASSOCIATED WITH THENUCLEAR MATRIX AT THE BASES OF THE CHROMATIN LOOPS

Special AT-rich sequence-binding protein 1 (SATB1), a DNA-binding prot ein expressed predominantly in thymocytes, recognizes an ATC sequence context that consists of a cluster of sequence stretches with well-mix ed A's, T's, and C's without Cr's on one strand. Such regions confer a high propensity for stable base unpairing. Using an in vivo cross-lin king strategy, specialized genomic sequences (0.1-1.1 kbp) that bind t o SATB1 in human lymphoblastic cell line Jurkat cells were individuall y Isolated and characterized. All in vivo SATB1-binding sequences exam ined contained typical ATC sequence contexts, with some exhibiting hom ology to autonomously replicating sequences from the yeast Saccharomyc es cerevisiae that function as replication origins in yeast cells. In addition, LINE 1 elements, satellite 2 sequences, and CpG island-conta ining DNA were identified. To examine the higher-order packaging of th ese in vivo SATB1-binding sequences, high-resolution in situ fluoresce nce hybridization was performed with both nuclear ''halos'' with diste nded loops and the nuclear matrix after the majority of DNA had been r emoved by nuclease digestion. In vivo SATB1-binding sequences hybridiz ed to genomic DNA as single spots within the residual nucleus circumsc ribed by the halo of DNA and remained as single spots in the nuclear m atrix, indicating that these sequences are localized at the base of ch romatin loops. In human breast cancer SK-BR-3 cells that do not expres s SATB1, at least one such sequence was found not anchored onto the nu clear matrix. These findings provide the first evidence that a cell ty pe-specific factor such as SATB1 binds to the base of chromatin loops in vivo and suggests that a specific chromatin loop domain structure i s involved in T cell-specific gene regulation.