Nucleome dynamics and histone priming by pioneer transcription factors drive osteoblast differentiation.

Functional maturation of osteoblasts from skeletal stem cells requires genome-wide transcriptional reprogramming, coincident with remodeling of transcribed (A) and inactive (B) chromatin compartments. Here, we assessed whether pioneer factor-driven histone activation links compartment remodeling to osteogenic transcriptional control. Integrative high-throughput 3D genome profiling analyses revealed that early reprogramming is governed by higher-order 3D genome regulation tightly coupled to A/B remodeling near osteogenic loci. Notably, B-to-A shifts were pre-marked in pre-osteoblasts by active histone modifications, indicative of histone priming, which was followed by gene activation upon osteogenic induction. Mechanistically, we identify ETS1 as a pioneer factor that recruits p300 (EP300) to establish histone activation-mediated priming and drive A-compartment shifts. This stage-specific regulation is evident in both cultured osteoblasts and during embryonic calvarial development in vivo. Our findings establish that pioneer factor-mediated histone priming contributes to global 3D genome reorganization to drive osteogenesis.