Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells.
Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells.
复制标题
DOI：
10.1016/j.stem.2018.06.014
复制
发表时间：
2018-08-02
期刊：
影响因子：
23.9
通讯作者：
Chambers I
中科院分区：
文献类型：
--
作者：
Barakat TS;Halbritter F;Zhang M;Rendeiro AF;Perenthaler E;Bock C;Chambers I
增强子是调控时空基因表达的遗传元件。增强子功能需要转录因子（TF）结合，并与组蛋白修饰相关。然而，TF结合和组蛋白修饰在功能上定义活性增强子的程度仍不清楚。在这里，我们将联合收割机染色质免疫沉淀与大规模平行报告基因检测（ChIP-STARR-seq）相结合，以定量无偏的方式在全基因组范围内鉴定人胚胎干细胞（ESC）中的功能增强子。尽管活性增强子与TF相关，但只有少数由NANOG、OCT 4、H3 K27 ac和H3 K4 me 1标记的区域起增强子的作用，在初始与引发培养条件下活性显著变化。我们确定了一个增强子集与扩展到非ESC特异性过程的功能。此外，尽管转座因子与假定的增强子相关，但只有一些表现出活性。类似地，在超级增强子中，大片段是非功能性的，活性仅限于小的亚结构域。这个目录的验证增强子提供了一个有价值的资源，进一步功能解剖的调控基因组。大规模平行报告基因分析评估了超过350，000个基因组区域ChIP-STARR-seq目录在引发和幼稚hESC中的功能增强子识别与增强子连接的转录因子和转座元件ChIP-STARR-seq将超级增强子分解为小功能单元Barakat et al.使用染色质免疫沉淀和大规模平行报告分析的组合来鉴定致敏和幼稚人类胚胎干细胞中的功能增强子。这种全基因组范围的验证增强子目录为进一步解剖调控基因组提供了宝贵的资源。
Enhancers are genetic elements that regulate spatiotemporal gene expression. Enhancer function requires transcription factor (TF) binding and correlates with histone modifications. However, the extent to which TF binding and histone modifications functionally define active enhancers remains unclear. Here, we combine chromatin immunoprecipitation with a massively parallel reporter assay (ChIP-STARR-seq) to identify functional enhancers in human embryonic stem cells (ESCs) genome-wide in a quantitative unbiased manner. Although active enhancers associate with TFs, only a minority of regions marked by NANOG, OCT4, H3K27ac, and H3K4me1 function as enhancers, with activity markedly changing under naive versus primed culture conditions. We identify an enhancer set associated with functions extending to non-ESC-specific processes. Moreover, although transposable elements associate with putative enhancers, only some exhibit activity. Similarly, within super-enhancers, large tracts are non-functional, with activity restricted to small sub-domains. This catalog of validated enhancers provides a valuable resource for further functional dissection of the regulatory genome. Massively parallel reporter assay assessed over 350,000 genome regions ChIP-STARR-seq catalogs functional enhancers in primed and naive hESCs Identification of transcription factors and transposable elements linked to enhancers ChIP-STARR-seq dissects super-enhancers into small functional units Barakat et al. use a combination of chromatin immunoprecipitation and a massively parallel reporter assay to identify functional enhancers in primed and naive human embryonic stem cells. This genome-wide catalog of validated enhancers provides a valuable resource for the further dissection of the regulatory genome.