A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells.
A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells.
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DOI：
10.1038/nmeth.4264
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发表时间：
2017-06
期刊：
影响因子：
48
通讯作者：
Ren B
中科院分区：
文献类型：
--
作者：
Diao Y;Fang R;Li B;Meng Z;Yu J;Qiu Y;Lin KC;Huang H;Liu T;Marina RJ;Jung I;Shen Y;Guan KL;Ren B
在人类基因组中预测了数以百万计的顺式调控元件，但关于它们生物学功能的直接证据仍然很少。在这里，我们报告了一种高通量的方法，即通过拼接-缺失和测序的顺式调节元件扫描(CREST-SEQ)，用于无偏见地发现和评估基因组中顺式调节序列的功能。我们用它来询问人类胚胎干细胞中的2MbpPou5f1基因座，并鉴定了Pou5f1的45个顺式调控元件。这些元素中的大多数都表现出活跃的染色质标记、DNA酶高敏感性和被多个转录因子占据，证实了染色质标记在顺式元件定位中的作用。值得注意的是，其中17个是先前注释的功能无关基因的启动子，并且像典型的增强子一样，它们与Pou5f1启动子形成了广泛的空间联系。综上所述，这些结果支持CREST-SEQ用于大规模顺式调控元件的发现，并指出人类基因组中增强子样启动子的共性。
Millions of cis-regulatory elements are predicted in the human genome, but direct evidence for their biological function is still scarce. Here we report a high-throughput method, Cis-Regulatory Element Scan by Tiling-deletion and sequencing (CREST-seq), for unbiased discovery and functional assessment of cis regulatory sequences in the genome. We use it to interrogate the 2Mbp POU5F1 locus in the human embryonic stem cells and identify 45 cis-regulatory elements of POU5F1. A majority of these elements display active chromatin marks, DNase hypersensitivity and occupancy by multiple transcription factors, confirming the utility of chromatin signatures in cis elements mapping. Notably, 17 of them are previously annotated promoters of functionally unrelated genes, and like typical enhancers, they form extensive spatial contacts with the POU5F1 promoter. Taken together, these results support the utility of CREST-seq for large-scale cis regulatory element discovery and point to commonality of enhancer-like promoters in the human genome.