Table 1. Transcriptional regulation of MEC differentiation –

Overall summary of bulk and scRNAseq expression profiles and their contribution to elucidating cellular state, master regulators, and lineage commitment across mammary epithelial tress.

Gene name	Cell types	Function	Identification method	References
Axin2	Multipotent cell fates	Lineage commitment and stemness	Lineage tracing, transplantation assays	[203,204]
BPTF	Basal epithelial cells, MaSC pool	MaSC self-renewal, ductal alveologenesis, regulation of chromatin accessibility	Gene knockdown, transgenic mice, RNA-seq, ATAC-seq	[231,333]
KDM5B	Luminal epithelial cells	Regulator of epigenetic and transcriptomic states	Single cell RNA-seq, mathematical and molecular modeling, gene knockdown, human tumor cell line cultures, inhibitor resistance	[206,207,211,213]
HOTAIR	Ductal carcinoma cells	Hormonal regulation of cell proliferation	Human tumor tissue analysis, microarray expression analysis, gene knockdown, PDX models	[263,264,266]
Let-7/miR-93/miR-200c	MaSCs	Maintenance of stemness and regulation of differentiation	3D cell culture assays, miRNA expression sequencing	[248]
NEAT1	Luminal ductal progenitors	Ductal morphogenesis throughout postnatal mammary development	Mouse tissue analysis, RNA in situ hybridization	[260,261]
PER2	MaSC pool	MaSC lineage commitment during pubertal development, regulation of MEC identity, epithelial-mesenchymal transition (EMT)	Transgenic mice, transplantation assays, RNA-seq,	[238,239]
PRC2 complex – EZH2	Luminal alveolar progenitors	Regulator of timing of differentiation and alveologenesis	Gene knockdown, transgenic mice, ES cell differentiation studies	[214,216,217]
PRC1 complex – Bmi1	MaSC pool	Mammary ductal expansion, alveolar cell differentiation, self-renewal of MaSCs	Human MaSC cultures, PDX models, transgenic mice	[218,243]
PROM1	ER+ luminal progenitors	Development and long-term homeostasis of ER+ luminal cells, alveologenesis	Transgenic mice, lineage tracing, transplantation assays	[334]
Pygo2	Basal epithelial cells, MaSC pool	MaSC self-renewal, regulation of chromatin accessibility, lineage commitment and differentiation	Gene knockdown, transgenic mice, transplantation assays, ChIP microarrays	[232,233,335]
SOX9	ER- luminal and basal progenitors	Development and long-term homeostasis of ER-luminal cells	Transgenic mice, lineage tracing, transplantation assays	[240,334]
STAT5	Luminal and basal progenitors	Lineage commitment and differentiation during pregnancy	Inhibitor assays, transgenic mice, microarray analysis, transplantation assays, 3D cell culture systems	[139,147,153–156,236,237]
miR-193b	Luminal progenitors	Control of MaSC activity and alveolar differentiation	Transplantation assays. RNA-seq, gene knockdown	[254]
miR-205/miR-22	MaSCs, MECs	Stemness, EMT, cell polarity, differentiation and specialization of MECs during late pregnancy through lactation, breast tumorigenesis	Transplantation assays, xenograft models, 3D cell culture, gene knockdown	[249–253]
miR-206/miR-150	Luminal alveolar cells, MaSCs	Regulation of cell proliferation, differentiation, and stemness during pregnancy, mammary positioning during embryogenesis	3D cell culture, microarray expression analysis, gene overexpression, transgenic mice	[255–257]
ZFAS1, PINC	Luminal alveolar cells	Terminal secretory differentiation during pregnancy and lactation, epigenetic control of mammary development	Gene knockdown, microarray expression analysis, RNA in situ hybridization	[259,261]