Department of Microbiology, New York University School of Medicine, New York, New York, USA.
Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York, USA.
Nat Methods. 2014 May;11(5):559-65. doi: 10.1038/nmeth.2885. Epub 2014 Mar 23.
Promoters and enhancers establish precise gene transcription patterns. The development of functional approaches for their identification in mammalian cells has been complicated by the size of these genomes. Here we report a high-throughput functional assay for directly identifying active promoter and enhancer elements called FIREWACh (Functional Identification of Regulatory Elements Within Accessible Chromatin), which we used to simultaneously assess over 80,000 DNA fragments derived from nucleosome-free regions within the chromatin of embryonic stem cells (ESCs) and identify 6,364 active regulatory elements. Many of these represent newly discovered ESC-specific enhancers, showing enriched binding-site motifs for ESC-specific transcription factors including SOX2, POU5F1 (OCT4) and KLF4. The application of FIREWACh to additional cultured cell types will facilitate functional annotation of the genome and expand our view of transcriptional network dynamics.
启动子和增强子建立精确的基因转录模式。由于这些基因组的大小，开发用于在哺乳动物细胞中鉴定它们的功能方法变得复杂。在这里，我们报告了一种称为 FIREWACh（可及染色质中调节元件的功能鉴定）的高通量功能测定法，用于直接鉴定活性启动子和增强子元件，我们使用它同时评估来自胚胎干细胞 (ESC) 染色质中无核小体区域的 80,000 多个 DNA 片段，并鉴定 6,364 个活性调节元件。其中许多代表新发现的 ESC 特异性增强子，显示出富含 ESC 特异性转录因子（包括 SOX2、POU5F1（OCT4）和 KLF4）结合位点的基序。FIREWACh 在其他培养细胞类型中的应用将有助于基因组的功能注释，并扩大我们对转录网络动态的认识。
