3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells [MEC_Omni-C]

In order to understand gene regulation of epithelial cells in the mouse mammary gland, we have generated a comprehensive epigenetic atlas from freshly sorted myoepithelial (basal), luminal progenitor (LP) and mature luminal (ML) from adult mice (9 week-old) encompassing gene expression profiling, histone and polymerase II CUT&Tag sequencing, chromatin accessibility via ATAC-seq and chromatin interactions. We further studied the basal compartment by sorting to additional cell type population: Tspan8+ (quiescent basal, QBa) and Tspan8- (active basal, ABa) cells. We then performed Omni-CTM, a DNase-based HiC protocol which measures the interaction frequency of all loci in the genome in duplicate of each of the sorted cellular populations from adult mice: myoepithelial (basal, Lin-/CD29hi/CD24+), luminal progenitor (LP, Lin-/CD29low/CD24+/CD61hi) and mature luminal (ML, Lin-/CD29low/CD24+/CD61low).