The RUNX2 Cistrome in Osteoblasts CHARACTERIZATION, DOWN-REGULATION FOLLOWING DIFFERENTIATION, AND RELATIONSHIP TO GENE EXPRESSION
The RUNX2 Cistrome in Osteoblasts CHARACTERIZATION, DOWN-REGULATION FOLLOWING DIFFERENTIATION, AND RELATIONSHIP TO GENE EXPRESSION
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DOI：
10.1074/jbc.m114.552216
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发表时间：
2014-06-06
影响因子：
4.8
通讯作者：
Pike, J. Wesley
中科院分区：
文献类型：
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作者：
Meyer, Mark B.;Benkusky, Nancy A.;Pike, J. Wesley
Runx2是一种转录因子，最早在早期成骨细胞系细胞中表达，是成骨细胞形成的主要决定因素。虽然许多靶基因受RUNX2调控，但对RUNX2在基因组上占据的位置或由这些位置控制的基因网络知之甚少。为了探索这一点，我们对成骨前MC3T3-E1细胞(POB)及其成熟成骨细胞后代(OB)中的RUNX2周期进行了全基因组分析，描述了这两个周期的特征，并评估了它们与基因表达变化的关系。我们发现，尽管RUNX2在POB细胞中广泛与基因组结合，但这种结合模式在分化为OBS时会减少。在分化过程中失去了许多部位，也获得了新的部位；许多部位对两种细胞状态都是共同的。还鉴定了其他特征，包括相对于潜在靶基因的位置，相对于单基因的丰度，经常存在一致的TGTGGT RUNX2结合基序，C/EBPβ共占，以及典型的表观遗传学组蛋白增强子特征的存在。这一特征在分化后发生了定量的变化。虽然RUNX2结合位点广泛地与相邻基因相关联，但大多数这些结合位点的远端性质阻碍了对它们是否代表RUNX2作用的直接靶点的评估。然而，基因表达的变化揭示了大量包含RUNX2结合位点的基因，并受到协同调控。这些研究为进一步分析RUNX2活性及其在成骨细胞系成熟过程中的功能奠定了基础。
RUNX2 is a transcription factor that is first expressed in early osteoblast-lineage cells and represents a primary determinant of osteoblastogenesis. While numerous target genes are regulated by RUNX2, little is known of sites on the genome occupied by RUNX2 or of the gene networks that are controlled by these sites. To explore this, we conducted a genome-wide analysis of the RUNX2 cistrome in both pre-osteoblastic MC3T3-E1 cells (POB) and their mature osteoblast progeny (OB), characterized the two cistromes and assessed their relationship to changes in gene expression. We found that although RUNX2 was widely bound to the genome in POB cells, this binding profile was reduced upon differentiation to OBs. Numerous sites were lost upon differentiation, new sites were also gained; many sites remained common to both cell states. Additional features were identified as well including location relative to potential target genes, abundance with respect to single genes, the frequent presence of a consensus TGTGGT RUNX2 binding motif, co-occupancy by C/EBP beta and the presence of a typical epigenetic histone enhancer signature. This signature was changed quantitatively following differentiation. While RUNX2 binding sites were associated extensively with adjacent genes, the distal nature of the majority of these sites prevented assessment of whether they represented direct targets of RUNX2 action. Changes in gene expression, however, revealed an abundance of genes that contained RUNX2 binding sites and were regulated in concert. These studies establish a basis for further analysis of the role of RUNX2 activity and its function during osteoblast lineage maturation.