van den Ameele Jelle, Trauner Manuel, Hörmanseder Eva, Donovan Alex P A, Llorà-Batlle Oriol, Cheetham Seth W, Krautz Robert, Yakob Rebecca, Malkowska Anna, Gurdon John B, Brand Andrea H
The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.
Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.
PLoS Biol. 2025 Mar 11;23(3):e3002944. doi: 10.1371/journal.pbio.3002944. eCollection 2025 Mar.
Histone modifications play a key role in regulating gene expression and cell fate during development and disease. Current methods for cell-type-specific genome-wide profiling of histone modifications require dissociation and isolation of cells and are not compatible with all tissue types. Here we adapt Targeted DamID (TaDa) to recognize specific histone marks, by fusing chromatin-binding proteins or single-chain antibodies to Dam, an Escherichia coli DNA adenine methylase. When combined with TaDa, this enables cell-type-specific chromatin profiling in intact tissues or organisms. We first profiled H3K4me3, H3K9ac, H3K27me3 and H4K20me1 in vivo in neural stem cells of the developing Drosophila brain. Next, we mapped cell-type-specific H3K4me3, H3K9ac and H4K20me1 distributions in the developing mouse brain. Finally, we injected RNA encoding DamID constructs into 1-cell stage Xenopus embryos to profile H3K4me3 distribution during gastrulation and neurulation. These results illustrate the versatility of TaDa to profile cell-type-specific histone marks throughout the genome in diverse model systems.
组蛋白修饰在发育和疾病过程中调节基因表达和细胞命运方面起着关键作用。目前用于细胞类型特异性全基因组组蛋白修饰分析的方法需要解离和分离细胞，并且并非适用于所有组织类型。在这里，我们通过将染色质结合蛋白或单链抗体与大肠杆菌DNA腺嘌呤甲基转移酶Dam融合，使靶向DamID（TaDa）能够识别特定的组蛋白标记。当与TaDa结合使用时，这能够在完整组织或生物体中进行细胞类型特异性染色质分析。我们首先在发育中的果蝇大脑的神经干细胞中对H3K4me3、H3K9ac、H3K27me3和H4K20me1进行了体内分析。接下来，我们绘制了发育中的小鼠大脑中细胞类型特异性的H3K4me3、H3K9ac和H4K20me1分布。最后，我们将编码DamID构建体的RNA注射到单细胞期非洲爪蟾胚胎中，以分析原肠胚形成和神经胚形成过程中H3K4me3的分布。这些结果说明了TaDa在不同模型系统中对全基因组细胞类型特异性组蛋白标记进行分析的多功能性。
