SOX–partner code for cell specification: Regulatory target selection and underlying molecular mechanisms

Transcriptional regulatory functions of SOX proteins generally require the cooperation of partner factors that bind DNA in the vicinity of the SOX site. Each SOX–partner pair selects a specific group of regulatory target genes, with resultant gene expression patterns characterizing a particular cell differentiation state. Specific examples include the SOX2–OCT3/4 pairing in ES cells and the SOX2–PAX6 pairing in visual system primordia. When a component of a SOX–partner pair is exchanged with another factor, an overt transition of gene expression occurs in a cell, leading to the progression of developmental processes. When a SOX–partner protein pair activates its own genes, the global cell/tissue state is stabilized. Two major molecular mechanisms underlie SOX–partner factor interactions: (1) cooperative DNA binding; and (2) protein interactions dependent upon DNA binding which elicit a large transactivation potential. In vivo evidence for and molecular mechanisms of the cell specification code attributed to the SOX–partner factor complexes are reviewed.