Abstract
Special AT-rich sequence-binding protein 1 (SATB1), a DNA-binding
protein expressed predominantly in thymocytes, recognizes an ATC
sequence context that consists of a cluster of sequence stretches
with well-mixed A's, T's, and C's without G's on one strand.
Such regions confer a high propensity for stable base unpairing.
Using an in vivo cross-linking strategy, specialized genomic sequences
(0.1-1. 1 kbp) that bind to SATB1 in human lymphoblastic cell line
Jurkat cells were individually isolated and characterized. All in
vivo SATB1-binding sequences examined contained typical ATC sequence
contexts, with some exhibiting homology to autonomously replicating
sequences from the yeast Saccharomyces cerevisiae that function as
replication origins in yeast cells. In addition, LINE 1 elements,
satellite 2 sequences, and CpG island-containing DNA were identified.
To examine the higher-order packaging of these in vivo SATB1-binding
sequences, high-resolution in situ fluorescence hybridization was
performed with both nuclear "halos" with distended loops and the
nuclear matrix after the majority of DNA had been removed by nuclease
digestion. In vivo SATB1-binding sequences hybridized to genomic
DNA as single spots within the residual nucleus circumscribed by
the halo of DNA and remained as single spots in the nuclear matrix,
indicating that these sequences are localized at the base of chromatin
loops. In human breast cancer SK-BR-3 cells that do not express SATB1,
at least one such sequence was found not anchored onto the nuclear
matrix. These findings provide the first evidence that a cell type-specific
factor such as SATB1 binds to the base of chromatin loops in vivo
and suggests that a specific chromatin loop domain structure is involved
in T cell-specific gene regulation.
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