Zusammenfassung
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.
- activation;
- analysis;
- animal;
- animals;
- binding
- biology,
- brain
- c57bl;
- calcitriol,
- ccaat-enhancer-binding
- cerebral
- chromatin
- computational
- cortex,
- disease
- female;
- genetic;
- genetics/pathology/physiopathology;
- genetics;
- humans;
- immunoprecipitation,
- inbred
- ischemia,
- logistic
- male;
- metabolism;
- methods;
- mice,
- mice;
- microarray
- models,
- models;
- molecular;
- physiology
- promoter
- protein-beta,
- receptors,
- regions,
- sites,
- transcriptional
- up-regulation,
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