Satb1 integrates DNA sequence, shape, motif density and torsional stress to differentially bind targets in nucleosome-dense regions.

Satb1 is a genome organizer that regulates multiple cellular and developmental processes. It is not yet clear how Satb1 selects different sets of targets throughout the genome. We used live-cell single molecule imaging and deep sequencing to assess determinants of Satb1 binding-site selectivity. We found that Satb1 preferentially targets nucleosome-dense regions and can directly bind consensus motifs within nucleosomes. Some genomic regions harbor multiple regularly spaced Satb1 binding motifs (typical separation ~1 turn of the DNA helix), characterized by highly cooperative binding. The Satb1 homeodomain is dispensable for high-affinity binding but is essential for specificity. Finally, Satb1⇔DNA interactions are mechanosensitive: increasing negative torsional stress in DNA enhances Satb1 binding and Satb1 stabilizes base unpairing regions (BURs) against melting by molecular machines. The ability of Satb1 to control diverse biological programs may reflect its ability to combinatorially use multiple site selection criteria.