Multi-omics approach revealed Pro-osteogenic properties of Barrier to antointegration factor 1 (BANF1)

Growth, remodeling, adaptation and repair of bone is critically dependent on the ability of tissue resident progenitors to differentiate into and thereby renew parenchymal cells of the osteoblast, chondrocyte, and adipocyte lineage. We recently reported that the activation of osteoblast-selective genes, such as alkaline phosphatase (ALPL), occurs through activation of pre-established enhancers, i.e., regulatory regions bound by transcriptional regulators prior to osteogenic induction. Using mass spectrometry-based quantitative proteomics, we identified 324 proteins with lineage-specific association to putative ALPL enhancer sequences during early osteoblast and adipocyte differentiation. Barrier to autointegration protein 1 (BANF1), known to be involved in chromatin compression and mutated in the Nestor-Guillermo progeria syndrome, was identified as a factor binding ALPL enhancers in an osteogenesis-selective manner. Using ChIP-seq analysis, we show here that BANF1associates with both structural and regulatory elements of the chromatin landscape in stromal cells and that BANF1 bound regulatory elements and nearby genes show increased activity upon osteogenic differentiation. Modulating BANF1 protein levels, first, alters expression of genes with nearby BANF1 binding, and second, strongly correlates with WNT signaling, osteogenic differentiation and bone forming capacity of the cells. Finally, genetic data reveal that the BANF1 locus harbors human sequence variations that correlate changes in bone mineral density and BANF1 expression while expression data from human bone related biopsies link decreased BANF1 expression with aging and osteoporosis. In conclusion, we identified BANF1 as a strong pro-osteogenic factor that is necessary for the maintenance of a cellular and molecular signature of osteoblast activity and bone formation in vivo. Overall design: BANF1 ChIP-seq experiments were carried out in human bone marrow derived and TERT immortalized marrow stromal cells (hBM-MSC-TERT-4 cells) at the undifferentiated state and after 1 day of osteogenic and adipogenic induction