Satb1 integrates DNA sequence, shape, motif density and torsional stress to selectively bind a subset of putative targets in nucleosome-dense regions of the genome

Satb1 (Special AT-rich sequence binding protein 1) coordinates chromatin architecture and regulates a diverse set of cellular and developmental processes. It is not yet clear how Satb1 selects it targets throughout the genome and which cellular parameters modulate its binding landscape. We have used single molecule live cell imaging and deep sequencing to quantify the arrangement of SatB1 molecules in the living nucleus and relate those spatial patterns to specific genomic features. We found that Satb1 preferentially binds to nucleosome dense regions and can access consensus motifs embedded in nucleosomes, features that epitomize 'pioneer' factors. Super-resolution live cell microscopy paired with deep sequencing showed that Satb1 binds iteratively to a set of closely clustered binding sites in the nucleus, and that binding is highly cooperative in regions with high motif density. Further, we observed that Satb1 uses DNA shape information from motif-flanking regions to narrow its binding spectrum. Satb1/DNA interactions were mechanosensitive. Increasing negative torsional stress enhanced binding and Satb1 stabilized base unpairing regions (BURs) against melting by molecular machines such as topoisomerases. Indeed, the ability of a small number of 'master' regulators to control diverse biological programs suggests that these regulators must use a multiparameter, combinatorial logic to select the cell-type and temporally appropriate chromatin state Analysis of the interaction of Satb1 and Chromatin by coupling various genomics tools and high resolution imaging