Oligomerization of SATB1 plays a very important role in DNA binding and has been implicated in gene regulation by SATB1. The structure of the SATB1 ULD domain reported here provides the molecular basis for how the ULD domain mediated the oligomerization state of SATB1. SATB1 assembles into a tetramer in vitro
(A), and the tetramerization of SATB1 is essential for recognizing specific DNA sequences (such as multiple AT-rich DNA fragments). Thus, SATB1 may regulate gene expression directly by binding to various promoters and upstream regions and thereby influencing promoter activity (B). This local gene regulation model is consistent with experimental observations that SATB1 directly regulates the expression of a number of genes, including globin, interleukin-2, interleukin-2 receptor α and interleukin-5, by recruiting either coactivators or corepressors (5–8
). Furthermore, we showed that the SATB1 tetramer can simultaneously bind to two DNA segments, and thus the tetramerization of SATB1 may organize high-order chromatin architecture by anchoring specialized DNA sequences in close proximity and recruiting various chromatin remodeling factors to coordinately regulate gene expression over long distances (C). This long-range gene regulation model is also consistent with the observations that SATB1 regulates the coordinated expression of genes located both at the 200-kb T-helper 2 cytokine locus (10
) and at the 300-kb major histocompatibility Class I locus (11
), and that it reprograms chromatin organization and the transcriptional profiles of breast tumors to promote growth and metastasis (12
Figure 5. Model of SATB1-mediated transcriptional regulation. (A) Schematic showing SATB1 assembles into a tetramer by oligomerization of its N-terminal ULD domain. (B and C) Schematic representation of a possible model for SATB1 oligomer-mediated transcriptional (more ...)
Long-range gene regulation plays a role in many biological activities such as regulation of the β-globin locus (33
), cytokine gene cluster (34
), estrogen-induced gene expression (35
) and mating-type switching in yeast (36
). Moreover, it has been found that the CI protein of bacteriophage λ regulates gene expression over a long distance via cooperative binding of its oligomers to specific target DNA (37
). Our proposed model for SATB1 oligomerization-mediated long-range gene regulation is consistent with their finding and likely represents a general mechanism for spatiotemporal and quantitative regulation of gene expression.
Any assembly of a functional protein complex in a living cell must be dynamically regulated. The oligomeric assembly of SATB1 is not an exception. The mechanism that regulates the dynamic assembly of SATB1 tetramers remains unclear. Understanding the dynamic regulatory assembly mechanism of SATB1 (or SATB2) is an important area of future research. SATB1 is known to be acetylated by P300/CBP-associated factor at residue Lys136, located just within the 136
N motif, which is important for SATB1 tetramerization and to mediate gene regulation in coordination with C-terminal-binding protein 1 during Wnt signaling in T cells (7
). The identification of key residues (i.e. 97
H and 136
N motifs) in the assembly of SATB1 oligomers (and likely SATB2) should be helpful in designing mutants of SATB family proteins to evaluate their functional roles in living cells and/or animal models.
The results of EMSA and ITC indicate that the ULD-mediated SATB1 oligomerization can affect the DNA-binding affinity and stoichiometry for SATB1 (). It is possible that, similar to DNA binding, the ULD-mediated SATB1 oligomerization may also affect the binding affinity and stoichiometry for its various protein-binding partners. Furthermore, the ITC data showed that SATB1 may allosterically bind to two DNA fragments, indicating that SATB1 binds to multiple AT-rich-containing DNA fragments with higher affinity by its tetramerization. In addition, a previous study suggested a rapid association and dissociation kinetics of DNA binding by SATB1 (3
). Whether the oligomerization of SATB1 influencing the kinetic constants of DNA-binding by SATB1 needs to be investigated in the future study by other technique such as surface plasmon resonance.
Although the N-terminus of SATB1 (residues 90–204) was previously identified as a PDZ domain (15
), structural studies have shown that this region is made up of ULD and CUTL domains. Detailed sequence alignments show that CUTL has the evolutionarily conserved amino acids involved in CUT1 DNA binding (Supplementary Figures S2B
). It would be interesting to investigate the functional role of the CUTL domain of SATB1 in future studies.