A quantitative model of transcription regulation reveals the role of non-conserved enhancers

We identify sites of combinatorial control by performing high throughput ChIP experiments on p300, CREB-binding protein (CBP), the deacetylase SIRT1 and on multiple DNA-binding transcription factors in three different tissues. We present a quantitative model of transcriptional regulation that reveals the contribution of each binding site to tissue-specific gene expression in several mouse cell types. Binding to both evolutionarily conserved and non-conserved sequences is found to contribute significantly to transcriptional regulation. We demonstrate that binding location strongly predicts the expression level of nearby genes. Liver hepatocytes and cerebellum tissue were harvested from male C57BL/6J mice. RNA was extracted and hybridized to Affymetrix arrays. Examination of transcriptional regulator binding in three mouse tissues by ChIP-IP using tiling arrays. Examination of CBP binding in mouse liver and cerebellum by ChIP-seq.本研究通过针对p300、CREB结合蛋白（CBP）、去乙酰化酶SIRT1以及多种DNA结合转录因子，在三种不同组织中开展高通量染色质免疫共沉淀（Chromatin Immunoprecipitation, ChIP）实验，鉴定得到组合调控位点。本研究构建了转录调控定量模型，揭示了各结合位点对多种小鼠细胞类型中组织特异性基因表达的调控贡献。研究表明，结合进化保守序列与非保守序列均对转录调控具有显著贡献。本研究证实，结合位点的位置可有效预测邻近基因的表达水平。实验取材于雄性C57BL/6J小鼠的肝实质细胞与小脑组织。提取RNA后与Affymetrix基因芯片进行杂交。采用平铺式芯片（tiling array）结合ChIP-IP技术，对三种小鼠组织内的转录调控因子结合情况进行检测。通过染色质免疫共沉淀测序（Chromatin Immunoprecipitation Sequencing, ChIP-seq）技术，对小鼠肝脏与小脑内的CBP结合状态进行检测。