The histone demethylase KDM6A controls the mammary luminal lineage through enzyme-independent mechanisms. Mus musculus

Mammary ducts and alveoli are composed of basal and luminal cells, with the fate and differentiation of secreting cells being controlled by hormones through specific transcription factors. This study establishes the essential role of the histone H3 lysine 27 trimethylation (H3K27me3) demethylase KDM6A (UTX) in obtaining a balanced compartment of basal and luminal cells. Deletion of Kdm6a in mammary stem cells led to a shift from luminal to basal cells and their excessive expansion that yielded disorganized ducts and alveoli and lactation failure. Mutant luminal cells lost their distinctive transcription factor expression pattern and acquired basal characteristics as demonstrated in mammosphere assays. The genomic H3K27me3 landscape was unaltered in the absence of KDM6A suggesting demethylase-independent mechanisms. In support of this, mammary tissue developed normally in the presence of a catalytically inactive KDM6A. ChIP-seq experiments demonstrated KDM6A binding to putative enhancers enriched for key mammary transcription factors and H3K27ac marks. Notably, the vast majority of KDM6A occupancy at promoter regions corresponded to Phantom peaks. This study demonstrated for the first time that mammary luminal cells rely on KDM6A to stably maintain their identity and ensure a transcriptional program leading to differentiated alveoli.