Genome organization by SATB1 binding to base-unpairing regions (BURs) provides a scaffold for SATB1-regulated gene expression

Mammalian genomes are organized by multi-level folding, yet how this organization contributes to cell type-specific transcription remain unclear. We uncovered that the nuclear protein SATB1 establishes two-tiered chromatin organization, one through indirect binding and another by direct binding of base-unpairing regions (BURs), which are genomic elements with high unwinding propensities. Published ChIP-seq datasets show SATB1 binding to highly accessible chromatin at enhancers and CTCF sites, but not to BURs. By employing urea ChIP-seq, which retains only directly bound protein:DNA complexes, we found that BURs, but not CTCF sites, are direct SATB1 binding targets. SATB1-bound BUR interactions with accessible chromatin can cross multiple topologically associated domains (TADs) and SATB1 is required for these megabase-scale interactions linked to cell type-specific gene expression. BURs are mainly found within lamina associated domains (LADs) sequestered at the nuclear lamina, but also in inter-LADs, and SATB1 binds a subset of BURs depending on cell type. Notably, despite the mutually exclusive SATB1-binding profiles uncovered by the two ChIP-seq methods, we found most peaks in both profiles are real and require SATB1. Together, we propose that SATB1 has functionally distinct modes of chromatin interaction by directly binding BURs to form a chromatin scaffold to which it indirectly tethers open chromatin. Such chromatin organization may provide a gene-regulatory network underlying cell type-specific gene expression.