During cell division, cessation of transcription is coupled with mitotic chromosome condensation. A fundamental biological question is how gene expression patterns are retained during mitosis to ensure the phenotype of progeny cells. We suggest that cell fate-determining transcription factors provide an epigenetic mechanism for the retention of gene expression patterns during cell division. Runx proteins are lineage-specific transcription factors that are essential for hematopoietic, neuronal, gastrointestinal, and osteogenic cell fates. Here we show that Runx2 protein is stable during cell division and remains associated with chromosomes during mitosis through sequence-specific DNA binding. Using siRNA-mediated silencing, mitotic cell synchronization, and expression profiling, we identify Runx2-regulated genes that are modulated postmitotically. Novel target genes involved in cell growth and differentiation were validated by chromatin immunoprecipitation. Importantly, we find that during mitosis, when transcription is shut down, Runx2 selectively occupies target gene promoters, and Runx2 deficiency alters mitotic histone modifications. We conclude that Runx proteins have an active role in retaining phenotype during cell division to support lineage-specific control of gene expression in progeny cells.L ineage commitment and cell proliferation are critical for normal tissue development. Preservation of phenotype during clonal expansion of committed cells necessitates the faithful segregation of chromosomes and the conveyance of lineage-specific gene regulatory machinery to progeny cells. Mitosis involves nuclear reorganization, global chromosome condensation, and transcription silencing and occurs concomitant with protein degradation and/or displacement of many regulatory factors from chromosomes (1-4). One fundamental question is how cells are programmed to sustain phenotypic gene expression patterns after cell division when transcriptional competency is restored in progeny cells.Cell fate is determined in response to extracellular cues by lineage-specific master regulators that include the Runx family of transcription factors. In mammals, these proteins are required for development of hematopoietic (Runx1), osteogenic (Runx2), and gastrointestinal and neuronal (Runx3) cell lineages (5-11). Runx factors integrate cell signaling pathways (e.g., TGF-/bone morphogenetic protein and Yes/Src) and recruit chromatin-modifying enzymes (e.g., histone deacetylases, histone acetyltransferases, SWI/SNF, SuVar139) to modulate promoter accessibility within a nucleosomal context (10,(12)(13)(14)(15)(16)(17). Runx proteins function as promoter-bound scaffolds that organize the regulatory machinery for gene expression within punctate subnuclear domains during interphase (18,19). Pathological perturbations in the organization of these domains are linked with altered development and tumorigenesis (10,(20)(21)(22)(23)(24)(25)(26)(27)(28)(29). Temporal and spatial changes of these architecturally organized Runx domains occur during...