a Department of Embryology, Carnegie Institution for Science Baltimore , Baltimore , MD , USA.
b Institute of Toxicology, College of Preventive Medicine, Third Military Medical University , Chongqing , PR China.
Epigenetics. 2019 Sep;14(9):877-893. doi: 10.1080/15592294.2019.1621139. Epub 2019 Jun 6.
Much effort has been devoted to understand how chromatin modification regulates development and disease. Despite recent progress, however, it remains difficult to obtain high-quality epigenomic maps using chromatin-immunoprecipitation-coupled deep sequencing (ChIP-seq) in samples with low-cell numbers. Here, we present an 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 acetylation (H3K27Ac) in group I innate lymphoid cells (ILC1) sorted from different tissues in parallel, aFARP-ChIP-seq uncovers putative active promoter and enhancer landscapes of several tissue-specific Natural Killer cells (NK) and ILC1. aFARP-ChIP-seq is also highly effective in mapping transcription factor binding sites in small number of cells. Thus, aFARP-ChIP-seq offers multiplexing mapping of both epigenome and transcription factor binding sites using a small number of cells.
人们投入了大量精力来了解染色质修饰如何调控发育和疾病。然而，尽管最近取得了一些进展，但在细胞数量较少的样本中，使用染色质免疫沉淀结合深度测序（ChIP-seq）获得高质量的表观基因组图谱仍然具有挑战性。在这里，我们提出了一种基于 Atlantis dsDNase 的技术，aFARP-ChIP-seq，它可以在少至 100 个细胞中准确地对全基因组组蛋白修饰进行分析。通过对从不同组织中分选的 I 型固有淋巴细胞（ILC1）进行组蛋白赖氨酸三甲基化（H3K4me3）和乙酰化（H3K27Ac）的平行作图，aFARP-ChIP-seq 揭示了几个组织特异性自然杀伤细胞（NK）和 ILC1 的潜在活性启动子和增强子景观。aFARP-ChIP-seq 还可以高效地在少量细胞中绘制转录因子结合位点。因此，aFARP-ChIP-seq 可以使用少量细胞对表观基因组和转录因子结合位点进行多重映射。
