Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq.
Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq.
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作者：
Zhou P;Gu F;Zhang L;Akerberg BN;Ma Q;Li K;He A;Lin Z;Stevens SM;Zhou B;Pu WT
了解调节细胞类型特异性转录程序的机制需要开发其基因组调节元件的词典。我们开发了一种谱系选择性方法来绘制小鼠体内转录增强子（激活转录的调控基因组区域）的图谱。由于大多数组织特异性增强子均与转录共激活子 Ep300 结合，因此我们使用 Cre 导向的谱系特异性 Ep300 生物素化和固定化链霉亲和素的下拉，然后对共沉淀 DNA 进行下一代测序来鉴定谱系特异性增强子。通过用谱系特异性 Cre 转基因驱动该系统，我们绘制了胚胎内皮细胞/血液或骨骼肌中活性增强子的图谱。对这些增强子的分析发现了可能调节这些谱系转录的新转录因子异二聚体基序。此外，我们还确定了调节成人心脏或肺特异性内皮细胞特化的候选增强子。我们的组织特异性蛋白质生物素化策略为研究谱系特异性蛋白质-DNA 和蛋白质-蛋白质相互作用开辟了新途径。 DOI：http://dx.doi.org/10.7554/eLife.22039.001
Understanding the mechanisms that regulate cell type-specific transcriptional programs requires developing a lexicon of their genomic regulatory elements. We developed a lineage-selective method to map transcriptional enhancers, regulatory genomic regions that activate transcription, in mice. Since most tissue-specific enhancers are bound by the transcriptional co-activator Ep300, we used Cre-directed, lineage-specific Ep300 biotinylation and pulldown on immobilized streptavidin followed by next generation sequencing of co-precipitated DNA to identify lineage-specific enhancers. By driving this system with lineage-specific Cre transgenes, we mapped enhancers active in embryonic endothelial cells/blood or skeletal muscle. Analysis of these enhancers identified new transcription factor heterodimer motifs that likely regulate transcription in these lineages. Furthermore, we identified candidate enhancers that regulate adult heart- or lung- specific endothelial cell specialization. Our strategy for tissue-specific protein biotinylation opens new avenues for studying lineage-specific protein-DNA and protein-protein interactions. DOI: http://dx.doi.org/10.7554/eLife.22039.001