Soldi Monica, Mari Tommaso, Nicosia Luciano, Musiani Daniele, Sigismondo Gianluca, Cuomo Alessandro, Pavesi Giulio, Bonaldi Tiziana
Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy.
Department of Biosciences, Milan University, Milan 20133, Italy.
Nucleic Acids Res. 2017 Dec 1;45(21):12195-12213. doi: 10.1093/nar/gkx821.
The integrated activity of cis-regulatory elements fine-tunes transcriptional programs of mammalian cells by recruiting cell type-specific as well as ubiquitous transcription factors (TFs). Despite their key role in modulating transcription, enhancers are still poorly characterized at the molecular level, and their limited DNA sequence conservation in evolution and variable distance from target genes make their unbiased identification challenging. The coexistence of high mono-methylation and low tri-methylation levels of lysine 4 of histone H3 is considered a signature of enhancers, but a comprehensive view of histone modifications associated to enhancers is still lacking. By combining chromatin immunoprecipitation (ChIP) with mass spectrometry, we investigated cis-regulatory regions in macrophages to comprehensively identify histone marks specifically associated with enhancers, and to profile their dynamics after transcriptional activation elicited by an inflammatory stimulation. The intersection of the proteomics data with ChIP-seq and RNA-seq analyses revealed the existence of novel subpopulations of enhancers, marked by specific histone modification signatures: specifically, H3K4me1/K36me2 marks transcribed enhancers, while H3K4me1/K36me3 and H3K4me1/K79me2 combinations mark distinct classes of intronic enhancers. Thus, our MS analysis of functionally distinct genomic regions revealed the combinatorial code of histone modifications, highlighting the potential of proteomics in addressing fundamental questions in epigenetics.
顺式调控元件的整合活性通过招募细胞类型特异性以及普遍存在的转录因子来微调哺乳动物细胞的转录程序。尽管增强子在调节转录中起关键作用，但在分子水平上其特征仍不明确，并且它们在进化中的有限DNA序列保守性以及与靶基因的可变距离使得对其进行无偏识别具有挑战性。组蛋白H3赖氨酸4的高单甲基化水平和低三甲基化水平的共存被认为是增强子的标志，但仍缺乏与增强子相关的组蛋白修饰的全面观点。通过将染色质免疫沉淀（ChIP）与质谱相结合，我们研究了巨噬细胞中的顺式调控区域，以全面鉴定与增强子特异性相关的组蛋白标记，并描绘炎症刺激引发转录激活后它们的动态变化。蛋白质组学数据与ChIP-seq和RNA-seq分析的交叉揭示了新型增强子亚群的存在，其以特定的组蛋白修饰特征为标志：具体而言，H3K4me1/K36me2标记转录的增强子，而H3K4me1/K36me3和H3K4me1/K79me2组合标记不同类别的内含子增强子。因此，我们对功能不同的基因组区域的质谱分析揭示了组蛋白修饰的组合密码，突出了蛋白质组学在解决表观遗传学基本问题方面的潜力。
