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Runx1 is highly expressed in osteoblasts, however, its function in osteogenesis is unclear. We generated mesenchymal progenitor-specific (Runx1f/fTwist2-Cre) and osteoblast-specific (Runx1f/fCol1α1-Cre) conditional knockout (Runx1 CKO) mice. The mutant CKO mice with normal skeletal development displayed a severe osteoporosis phenotype at postnatal and adult stages. Runx1 CKO resulted in decreased osteogenesis and increased adipogenesis. RNA-sequencing analysis, Western blot, and qPCR validation of Runx1 CKO samples showed that Runx1 regulates BMP signaling pathway and Wnt/β-catenin signaling pathway. ChIP assay revealed direct binding of Runx1 to the promoter regions of Bmp7, Alk3, and Atf4, and promoter mapping demonstrated that Runx1 upregulates their promoter activity through the binding regions. Bmp7 overexpression rescued Alk3, Runx2, and Atf4 expression in Runx1-deficient BMSCs. Runx2 expression was decreased while Runx1 was not changed in Alk3 deficient osteoblasts. Atf4 overexpression in Runx1-deficient BMSCs did not rescue expression of Runx1, Bmp7, and Alk3. Smad1/5/8 activity was vitally reduced in Runx1 CKO cells, indicating Runx1 positively regulates the Bmp7/Alk3/Smad1/5/8/Runx2/ATF4 signaling pathway. Notably, Runx1 overexpression in Runx2-/- osteoblasts rescued expression of Atf4, OCN, and ALP to compensate Runx2 function. Runx1 CKO mice at various osteoblast differentiation stages reduced Wnt signaling and caused high expression of C/ebpα and Pparγ and largely increased adipogenesis. Co-culture of Runx1-deficient and wild-type cells demonstrated that Runx1 regulates osteoblast−adipocyte lineage commitment both cell-autonomously and non-autonomously. Notably, Runx1 overexpression rescued bone loss in OVX-induced osteoporosis. This study focused on the role of Runx1 in different cell populations with regards to BMP and Wnt signaling pathways and in the interacting network underlying bone homeostasis as well as adipogenesis, and has provided new insight and advancement of knowledge in skeletal development. Collectively, Runx1 maintains adult bone homeostasis from bone loss though up-regulating Bmp7/Alk3/Smad1/5/8/Runx2/ATF4 and WNT/β-Catenin signaling pathways, and targeting Runx1 potentially leads to novel therapeutics for osteoporosis., Author summary Bone loss in osteoporosis and many other degenerative bone diseases is characterized by decreased bone formation and increased fat accumulation in the bone marrow, especially during aging, and many are suspected to have a genetic basis. Bone marrow mesenchymal stem cells (BMSCs) can differentiate into adipocytes, chondrocytes, and osteoblasts. BMSCs from aging or genetic defect subjects are less likely to differentiate into osteoblasts while more inclined to differentiate into adipocytes. However, the molecular mechanisms remain elusive. Here, we describe a new mutant mice model-Runx1 mesenchymal progenitor-specific and osteoblast-specific conditional knockout (Runx1 CKO) mice, which showed the severe bone formation defects and adipocytes accumulation. Here, we revealed that Runx1 enhances osteoblast lineage commitment promotes bone formation and inhibits adipogenesis by up-regulating the Bmp7/Alk3/Smad1/5/8/Runx2/ATF4 and WNT/β-catenin signaling pathways and orchestrating multiple signaling pathways involved in bone formation. These findings further elucidated the roles of Runx1 in bone homeostasis with implications into development of novel therapeutic strategies for osteoporosis as well as other degenerative bone diseases.