Chen Zhiyuan, Zhang Chunxia, Zhang Yi
Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
Department of Genetics, Harvard Medical School, Boston, MA, USA.
Methods Mol Biol. 2025;2923:33-44. doi: 10.1007/978-1-0716-4522-2_3.
Extensive chromatin reprogramming after fertilization is essential for successful zygotic genome activation (ZGA) and embryonic development. Traditional chromatin profiling techniques chromatin immunoprecipitation assay with sequencing (ChIP-seq) and deoxyribonuclease I hypersensitivity sequencing (DNase-seq) require large number of cells, which are not suitable for rare biological materials such as mammalian preimplantation embryos. Recent advancement of low-input epigenome profiling techniques has allowed the exploration of chromatin dynamics and functions during ZGA and early embryonic development. In this chapter, we describe two low-input methods, namely, CUT&RUN and ATAC-seq, that are efficient and robust for chromatin analyses using as few as 50-100 cells. These methods are useful for profiling histone modifications, histone variants, and chromatin accessibility in mammalian preimplantation studies.
受精后广泛的染色质重编程对于成功的合子基因组激活（ZGA）和胚胎发育至关重要。传统的染色质分析技术，如染色质免疫沉淀测序（ChIP-seq）和脱氧核糖核酸酶I超敏测序（DNase-seq），需要大量细胞，这不适合诸如哺乳动物植入前胚胎等稀有生物材料。低投入表观基因组分析技术的最新进展使得在ZGA和早期胚胎发育过程中对染色质动力学和功能的探索成为可能。在本章中，我们描述了两种低投入方法，即CUT&RUN和ATAC-seq，它们对于使用少至50-100个细胞进行染色质分析高效且稳健。这些方法对于在哺乳动物植入前研究中分析组蛋白修饰、组蛋白变体和染色质可及性很有用。
