Kreibich Elisa, Kleinendorst Rozemarijn, Barzaghi Guido, Kaspar Sarah, Krebs Arnaud R
European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany.
European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
Mol Cell. 2023 Mar 2;83(5):787-802.e9. doi: 10.1016/j.molcel.2023.01.017. Epub 2023 Feb 8.
Enhancers are cis-regulatory elements that control the establishment of cell identities during development. In mammals, enhancer activation is tightly coupled with DNA demethylation. However, whether this epigenetic remodeling is necessary for enhancer activation is unknown. Here, we adapted single-molecule footprinting to measure chromatin accessibility and transcription factor binding as a function of the presence of methylation on the same DNA molecules. We leveraged natural epigenetic heterogeneity at active enhancers to test the impact of DNA methylation on their chromatin accessibility in multiple cell lineages. Although reduction of DNA methylation appears dispensable for the activity of most enhancers, we identify a class of cell-type-specific enhancers where DNA methylation antagonizes the binding of transcription factors. Genetic perturbations reveal that chromatin accessibility and transcription factor binding require active demethylation at these loci. Thus, in addition to safeguarding the genome from spurious activation, DNA methylation directly controls transcription factor occupancy at active enhancers.
增强子是顺式调控元件，在发育过程中控制细胞身份的建立。在哺乳动物中，增强子激活与DNA去甲基化紧密相关。然而，这种表观遗传重塑对于增强子激活是否必要尚不清楚。在这里，我们采用单分子足迹法来测量染色质可及性和转录因子结合，作为同一DNA分子上甲基化存在情况的函数。我们利用活跃增强子处的自然表观遗传异质性，来测试DNA甲基化对其在多个细胞谱系中染色质可及性的影响。尽管DNA甲基化的减少对于大多数增强子的活性似乎并非必需，但我们鉴定出一类细胞类型特异性增强子，其中DNA甲基化拮抗转录因子的结合。基因扰动表明，染色质可及性和转录因子结合在这些位点需要活跃的去甲基化。因此，除了保护基因组免受虚假激活外，DNA甲基化还直接控制活跃增强子处转录因子的占据。
