Fig. 1.

Loss of nuclear matrix protein 4 (Nmp4) accelerates and enhances mesenchymal stem/progenitor cell (MSPC) mineralization and has a broad impact on the transcriptome. A: 6 independently expanded MSPC preparations from individual wild-type (WT) and Nmp4^−/− mice were established as described in materials and methods. Cultures were stained with alizarin red when mineralization was first observed. The cells derived from the Nmp4^−/− mice consistently exhibited mineral days to weeks before this was observed in the WT cultures. The cell preparations 1957N^KO and 1957R^WT were derived from male littermates. The remaining lines were derived from male or female mice selected from random litters. B: volcano plots of RNA sequencing (RNA-seq) data from MSPCs maintained in nondifferentiating culture medium for 3 days and osteogenic differentiating culture medium for 7 days. The x-axis represents the logarithmic transformation to the base 2 of the mean fold change of mRNA expression in Nmp4^−/− cells versus control cells and the y-axis represents the negative logarithm to the base 10 of the false discovery rate (FDR) value. Changes in gene expression were considered significant if the fold change of knockout (KO)/WT greater than or equal to +2 (red circles) and FDR ≤0.05 or KO/WT less than or equal to −2 (green circles) and FDR ≤0.05. The black circles represent genes that did not meet either criterion. The dotted line demarcates FDR = 0.05. C: Venn diagrams showing gene overlap between chromatin immunoprecipitation sequencing (ChIP-seq) and RNA-seq data. The former was derived from MC3T3-E1 cells (16). Genes that supported Nmp4 occupancy were required to exhibit peaks (height ≥10) within 5 to +2 kb from a transcription start site (TSS) and/or located within the range defined by the TSS and the transcription end site.