Enhancer and transcription factor dynamics within the granulocytic-monocytic lineage reveal an early differentiation block in Cebpa null progenitors

Myeloid cells of the granulocytic-monocytic (GM) lineage develop in a process orchestrated mainly by the transcription factors PU.1 and CEBPA, but how these factors collaborate on a global scale during GM-lineage differentiation remains uncharacterized. To address this question we have combined epigenetic profiling, transcription factor binding and gene expression analyses of successive stages of murine GM-lineage differentiation and show that PU.1 and CEBPA binds to GM enhancers with distinct kinetics. Surprisingly, we find no evidence of a pioneering function of PU.1 during GM-lineage differentiation but instead delineate a set of GM enhancers that appears to open in a CEBPA-dependent manner. Analyses of Cebpa null bone marrow demonstrate that CEBPA controls PU.1 levels and, unexpectedly, that the loss of CEBPA results in a very early differentiation block. These data are consistent with a model involving an extensive functional interplay between PU.1 and CEBPA in driving GM-lineage differentiation. Examined 2 replicates each of H3K4me1, H3K27ac histone marks, 2 replicates each of PU.1 and CEBPA transcription factors across four granulocytic-monocytic differentiation stages and CEBPA KO condition Examined transcriptome from LSK, preGMs, GMP, CFU-G, CFU-M, granulocytes and monocytes in biological triplicates