An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations
An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations
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DOI：
10.1038/ncomms7033
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发表时间：
2015-01-01
影响因子：
16.6
通讯作者：
Lorincz, Matthew C.
中科院分区：
文献类型：
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作者：
Brind'Amour, Julie;Liu, Sheng;Lorincz, Matthew C.
结合染色质免疫沉淀和下一代测序（ChIP-seq）已经能够对许多细胞系和组织类型进行全基因组表观遗传分析。然而，ChIP-seq的一个主要限制是需要大量的细胞来生成高质量的数据集，从而排除了对稀有细胞群的研究。在这里，我们提出了一种超低输入的微球菌核酸酶为基础的天然ChIP（ULI-NChIP）和测序方法，以产生全基因组组的组蛋白标记配置文件，具有高分辨率，从103个细胞。我们证明了ULI-NChIP-seq可以从103到106个胚胎干细胞中生成高质量的共价组蛋白标记图。随后，我们表明，从单个男性和女性胚胎分离的E13.5原始生殖细胞生成的ULI-NChIP-seq H3 K27 me 3图谱与使用50-180倍以上材料生成的最近数据集具有高度相似性。最后，我们确定性二态H3 K27 me 3富集在特定的基因启动子，从而说明了这种方法的效用，从稀有细胞群体产生高质量和复杂的库。
Combined chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) has enabled genome-wide epigenetic profiling of numerous cell lines and tissue types. A major limitation of ChIP-seq, however, is the large number of cells required to generate high-quality data sets, precluding the study of rare cell populations. Here, we present an ultra-low-input micrococcal nuclease-based native ChIP (ULI-NChIP) and sequencing method to generate genome-wide histone mark profiles with high resolution from as few as 103 cells. We demonstrate that ULI-NChIP-seq generates high-quality maps of covalent histone marks from 103 to 106 embryonic stem cells. Subsequently, we show that ULI-NChIP-seq H3K27me3 profiles generated from E13.5 primordial germ cells isolated from single male and female embryos show high similarity to recent data sets generated using 50-180 x more material. Finally, we identify sexually dimorphic H3K27me3 enrichment at specific genic promoters, thereby illustrating the utility of this method for generating high-quality and -complexity libraries from rare cell populations.