Joint Binding of OTX2 and MYC in Promotor Regions Is Associated with High Gene Expression in Medulloblastoma

Both OTX2 and MYC are important oncogenes in medulloblastoma, the most common malignant brain tumor in childhood. Much is known about MYC binding to promoter regions, but OTX2 binding is hardly investigated. We used ChIP-on-chip data to analyze the binding patterns of both transcription factors in D425 medulloblastoma cells. When combining the data for all promoter regions in the genome, OTX2 binding showed a remarkable bi-modal distribution pattern with peaks around −250 bp upstream and +650 bp downstream of the transcription start sites (TSSs). Indeed, 40.2% of all OTX2-bound TSSs had more than one significant OTX2-binding peak. This OTX2-binding pattern was very different from the TSS-centered single peak binding pattern observed for MYC and other known transcription factors. However, in individual promoter regions, OTX2 and MYC have a strong tendency to bind in proximity of each other. OTX2-binding sequences are depleted near TSSs in the genome, providing an explanation for the observed bi-modal distribution of OTX2 binding. This contrasts to the enrichment of E-box sequences at TSSs. Both OTX2 and MYC binding independently correlated with higher gene expression. Interestingly, genes of promoter regions with multiple OTX2 binding as well as MYC binding showed the highest expression levels in D425 cells and in primary medulloblastomas. Genes within this class of promoter regions were enriched for medulloblastoma and stem cell specific genes. Our data suggest an important functional interaction between OTX2 and MYC in regulating gene expression in medulloblastoma.OTX2与MYC均为髓母细胞瘤（medulloblastoma，儿童最常见的恶性脑肿瘤）中关键的致癌基因（oncogenes）。学界对MYC结合启动子区域（promoter regions）的机制已有较为充分的研究，但针对OTX2结合模式的探究却鲜有报道。本研究利用染色质免疫沉淀芯片（ChIP-on-chip）数据，分析了D425髓母细胞瘤细胞中两种转录因子（transcription factors）的结合模式。当整合基因组中所有启动子区域的相关数据时，OTX2结合呈现出显著的双峰分布模式，其结合峰分别位于转录起始位点（transcription start sites, TSSs）上游约-250 bp与下游约+650 bp处。研究显示，40.2%的被OTX2结合的转录起始位点存在至少一个以上的显著OTX2结合峰。该OTX2结合模式与MYC及其他已知转录因子所呈现的、以转录起始位点为中心的单峰结合模式截然不同。不过，在单个启动子区域内，OTX2与MYC表现出极强的邻近结合倾向。基因组中转录起始位点附近的OTX2结合序列存在缺失现象，这一特征可解释OTX2结合的双峰分布格局，该现象与E-box序列（E-box sequences）在转录起始位点处的富集特征形成鲜明对比。OTX2与MYC的结合均与更高水平的基因表达（gene expression）呈独立相关。值得注意的是，同时存在多个OTX2结合位点与MYC结合位点的启动子区域所调控的基因，在D425细胞与原发性髓母细胞瘤（primary medulloblastomas）样本中均呈现出最高的表达水平。此类启动子区域所关联的基因，显著富集于髓母细胞瘤相关基因与干细胞特异性基因（stem cell specific genes）范畴。本研究数据表明，OTX2与MYC在调控髓母细胞瘤基因表达的过程中存在重要的功能协同作用。