A chromatin integration labelling method enables epigenomic profiling with lower input
A chromatin integration labelling method enables epigenomic profiling with lower input
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DOI：
10.1038/s41556-018-0248-3
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发表时间：
2019-02-01
影响因子：
21.3
通讯作者：
Ohkawa, Yasuyuki
中科院分区：
文献类型：
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作者：
Harada, Akihito;Maehara, Kazumitsu;Ohkawa, Yasuyuki
染色质在基因调控中起着至关重要的作用，染色质免疫沉淀随后测序（ChIP-seq）已经成为检测整个基因组中蛋白质- dna相互作用的标准技术。然而，由于染色质制备过程中的样品丢失和免疫沉淀效率低下，ChIP-seq很难从有限数量的细胞中获得表观基因组信息。在本研究中，我们建立了一种无免疫沉淀的表观基因组分析方法，称为染色质整合标记（ChIL），该方法可以在细胞裂解前扩增与靶分子密切相关的基因组序列。使用ChIL-seq (ChIL-seq)，我们可靠地检测了100- 1000个细胞中组蛋白修饰和dna结合因子的分布。此外，ChIL-seq成功地在单细胞水平检测到与组蛋白标记相关的基因组区域。因此，ChIL-seq提供了一种替代ChIP-seq的方法，使用少量细胞进行表观基因组分析，特别是那些附着在培养板上并经过免疫荧光的细胞。
Chromatin plays a crucial role in gene regulation, and chromatin immunoprecipitation followed by sequencing (ChIP-seq) has been the standard technique for examining protein-DNA interactions across the whole genome. However, it is difficult to obtain epigenomic information from limited numbers of cells by ChIP-seq because of sample loss during chromatin preparation and inefficient immunoprecipitation. In this study, we established an immunoprecipitation-free epigenomic profiling method named chromatin integration labelling (ChIL), which enables the amplification of genomic sequences closely associated with the target molecules before cell lysis. Using ChIL followed by sequencing (ChIL-seq), we reliably detected the distributions of histone modifications and DNA-binding factors in 100-1,000 cells. In addition, ChIL-seq successfully detected genomic regions associated with histone marks at the single-cell level. Thus, ChIL-seq offers an alternative method to ChIP-seq for epigenomic profiling using small numbers of cells, in particular, those attached to culture plates and after immunofluorescence.