Ridder Dirk A, Bulashevska Svetlana, Chaitanya Ganta Vijay, Babu Phanithi Prakash, Brors Benedikt, Eils Roland, Schneider Armin, Schwaninger Markus
Department of Pharmacology, University of Heidelberg, Germany.
Brain Res. 2009 May 26;1272:3-13. doi: 10.1016/j.brainres.2009.03.046. Epub 2009 Mar 31.
In stroke, gene transcription plays a central role in processes such as neuroinflammation and neuroregeneration. To predict new transcriptional regulatory mechanisms in cerebral ischemia, we applied a computational approach combining two kinds of information: the results of a microarray analysis in a mouse model of stroke and in silico detection of transcription factor (TF) binding sites in promoter regions of the genes on the array. By using a discriminative logistic regression model, we identified binding sites significantly associated with the up-regulation of genes. Out of 356 TF binding sites defined in TRANSFAC, we could link 32 to gene up-regulation in cerebral ischemia. These sites bind both TFs with an established and a so far unknown role in cerebral ischemia. To evaluate the results further we investigated whether two TFs, CCAAT/enhancer binding protein beta (C/EBP beta) and vitamin D receptor (VDR), are activated as predicted. Immunohistochemistry demonstrated that C/EBP beta and VDR translocated to the nucleus in cerebral ischemia. Chromatin immunoprecipitation revealed increased binding of C/EBP beta to the promoter of its target gene saa3. In addition, we found evidence for the up-regulation of VDR in brain samples from human stroke patients. These results confirm the activation of C/EBP beta and VDR in cerebral ischemia. Thus, our in silico analysis may provide additional information on transcriptional regulation in stroke and suggests several novel transcriptional programs for further exploration.
在中风中，基因转录在神经炎症和神经再生等过程中起着核心作用。为了预测脑缺血中新的转录调控机制，我们应用了一种计算方法，该方法结合了两种信息：中风小鼠模型中的微阵列分析结果以及阵列上基因启动子区域转录因子（TF）结合位点的计算机模拟检测。通过使用判别逻辑回归模型，我们确定了与基因上调显著相关的结合位点。在TRANSFAC中定义的356个TF结合位点中，我们可以将32个与脑缺血中的基因上调联系起来。这些位点结合的TF在脑缺血中既有已确定的作用，也有迄今未知的作用。为了进一步评估结果，我们研究了两种TF，即CCAAT/增强子结合蛋白β（C/EBPβ）和维生素D受体（VDR），是否如预测的那样被激活。免疫组织化学表明，C/EBPβ和VDR在脑缺血时易位至细胞核。染色质免疫沉淀显示C/EBPβ与其靶基因saa3启动子的结合增加。此外，我们发现了人类中风患者脑样本中VDR上调的证据。这些结果证实了C/EBPβ和VDR在脑缺血中的激活。因此，我们的计算机模拟分析可能会提供有关中风转录调控的额外信息，并提出几个新的转录程序以供进一步探索。
