Key message

Application of a low-input chromatin profiling method, CUT&RUN, to FACS-purified Arabidopsis endosperm nuclei generates parental-specific genome-wide H3K27me3 landscapes with high sensitivity, specificity and reproducibility.

Abstract

Endosperm is an essential seed tissue with a unique epigenetic landscape. During endosperm development, differential epigenetic regulation of the maternal and paternal genomes plays important roles in regulating gene expression, especially at imprinted genes. In Arabidopsis, profiling the epigenetic landscape of endosperm on a genome-wide scale is challenging due to its small size, mode of development and close association with maternal tissue. Here, we applied a low-input chromatin profiling method, CUT&RUN (cleavage under targets and release using nuclease), to profile parental-specific chromatin modifications using limited numbers of Arabidopsis endosperm nuclei. We demonstrate that CUT&RUN generates genome-wide H3K27me3 landscapes with high sensitivity, specificity and reproducibility using around 20,000 endosperm nuclei purified by flow cytometry and fluorescence-activated cell sorting. H3K27me3 peaks identified by CUT&RUN and previous ChIP (chromatin immunoprecipitation) approaches were largely overlapping, with some distinctions in heterochromatin. The versatility and simplicity of CUT&RUN make it a viable alternative to ChIP, which requires greater amounts of starting material, and will enable further study of tissue- or cell-type-specific epigenomes in Arabidopsis and other plant species.

中文翻译：

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使用CUT＆RUN在拟南芥胚乳中进行低输入染色质分析。

关键信息

在FACS纯化的拟南芥胚乳核中使用低输入染色质谱分析方法CUT＆RUN可以生成具有高灵敏度，特异性和可重复性的亲本特异性全基因组H3K27me3景观。

抽象

胚乳是具有独特表观遗传景观的重要种子组织。在胚乳发育过程中，母体和父本基因组的不同表观遗传调控在调控基因表达（尤其是在印迹基因中）方面起着重要作用。在拟南芥中，由于其体积小，发育方式以及与母体组织的紧密联系，因此要在全基因组范围内对胚乳的表观遗传学概况进行分析是一项挑战。在这里，我们应用了一种低输入量的染色质分析方法，即CUT＆RUN（在靶标下裂解并使用核酸酶释放），以使用有限数量的拟南芥胚乳核来分析亲本特异性的染色质修饰。我们证明了CUT＆RUN使用大约20种方法可以产生具有高灵敏度，特异性和可重复性的全基因组H3K27me3景观，通过流式细胞仪和荧光激活细胞分选纯化000个胚乳核。通过CUT＆RUN和以前的ChIP（染色质免疫沉淀）方法鉴定的H3K27me3峰在很大程度上重叠，在异染色质上有一些区别。CUT＆RUN的多功能性和简便性使其成为ChIP的可行替代方案，后者需要大量的起始原料，并将能够进一步研究拟南芥和其他植物物种中特定于组织或细胞类型的表观基因组。