aFARP-ChIP-seq, a convenient and reliable method for genome profiling in as few as 100 cells with a capability for multiplexing ChIP-seq
aFARP-ChIP-seq, a convenient and reliable method for genome profiling in as few as 100 cells with a capability for multiplexing ChIP-seq
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aFARP-ChIP-seq，一种方便可靠的方法，可在少至 100 个细胞中进行基因组分析，具有多重 ChIP-seq 的能力
DOI：
10.1080/15592294.2019.1621139
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发表时间：
2019
期刊：
影响因子：
3.7
通讯作者：
Yixian Zheng
中科院分区：
文献类型：
--
作者：
Wenbin Liu;Sibiao Yue;Xiaobin Zheng;Minjie Hu;Jia Cao;Yixian Zheng
人们一直致力于了解染色质修饰如何调节发育和疾病。然而，尽管最近取得了进展，染色质免疫沉淀耦合深度测序（ChIP-seq）在低细胞丰度细胞群体中绘制表观基因组和全局转录因子结合位点仍然难以实现高灵敏度和可靠性。我们提出了一种新的基于Atlantis dsdase的技术，aFARP-ChIP-seq，该技术可在少至100个细胞中提供全基因组组蛋白修饰的准确分析。通过绘制来自不同组织的I组先天淋巴样细胞中组蛋白赖氨酸三甲基化（H3K4me3）和H3K27Ac的图谱，aFARP-ChIP-seq揭示了几种组织特异性NK和ILC1的潜在不同的活性启动子和增强子。aFARP-ChIP-seq在少量细胞中定位转录因子结合位点也非常有效。由于aFARP-ChIP-seq提供了可复制的DNA片段，它应该允许对低细胞样本进行组蛋白修饰和转录因子结合位点的多重ChIP-seq。
Much effort has been devoted to understand how chromatin modification regulates development and disease. Despite recent progress, however, it remains difficult to achieve high sensitivity and reliability of chromatin-immunoprecipitation-coupled deep sequencing (ChIP-seq) to map the epigenome and global transcription factor binding sites in cell populations of low cell abundance. We present a new Atlantis dsDNase-based technology, aFARP-ChIP-seq, that provides accurate profiling of genome-wide histone modifications in as few as 100 cells. By mapping histone lysine trimethylation (H3K4me3) and H3K27Ac in group I innate lymphoid cells from different tissues, aFARP-ChIP-seq uncovers potentially distinct active promoter and enhancer landscapes of several tissue-specific NK and ILC1. aFARP-ChIP-seq is also highly effective in mapping transcription factor binding sites in small number of cells. Since aFARP-ChIP-seq offers reproducible DNA fragmentation, it should allow multiplexing ChIP-seq of both histone modifications and transcription factor binding sites for low cell samples.