Junion Guillaume, Jagla Teresa, Duplant Sebastien, Tapin Romain, Da Ponte Jean-Philippe, Jagla Krzysztof
Institut National de la Santé et de la Recherche Médicale Unité 384, Faculté de Médecine, 28 Place Henri Dunant, 63000 Clermont-Ferrand, France.
Proc Natl Acad Sci U S A. 2005 Dec 20;102(51):18479-84. doi: 10.1073/pnas.0507030102. Epub 2005 Dec 9.
Mapping the regulatory modules to which transcription factors bind in vivo is a key step toward understanding of global gene expression programs. We have developed a chromatin immunoprecipitation (ChIP)-chip strategy for identifying factor-specific regulatory regions acting in vivo. This method, called the ChIP-enriched in silico targets (ChEST) approach, combines immunoprecipitation of cross-linked protein-DNA complexes (X-ChIP) with in silico prediction of targets and generation of computed DNA microarrays. We report the use of ChEST in Drosophila to identify several previously unknown targets of myocyte enhancer factor 2 (MEF2), a key regulator of myogenic differentiation. Our approach was validated by demonstrating that the identified sequences act as enhancers in vivo and are able to drive reporter gene expression specifically in MEF2-positive muscle cells. Presented here, the ChEST strategy was originally designed to identify regulatory modules in Drosophila, but it can be adapted for any sequenced and annotated genome.
绘制转录因子在体内结合的调控模块图谱是理解全局基因表达程序的关键一步。我们开发了一种染色质免疫沉淀（ChIP）-芯片策略，用于识别在体内起作用的因子特异性调控区域。这种方法称为ChIP富集计算机预测靶点（ChEST）方法，它将交联的蛋白质-DNA复合物的免疫沉淀（X-ChIP）与靶点的计算机预测以及计算DNA微阵列的生成相结合。我们报告了在果蝇中使用ChEST来鉴定肌细胞增强因子2（MEF2）的几个先前未知的靶点，MEF2是成肌分化的关键调节因子。我们通过证明所鉴定的序列在体内作为增强子起作用并且能够特异性地驱动报告基因在MEF2阳性肌肉细胞中表达，验证了我们的方法。本文介绍的ChEST策略最初设计用于在果蝇中识别调控模块，但它可以适用于任何已测序和注释的基因组。
