A UTX–MLL4–p300 Transcriptional Regulatory Network Coordinately Shapes Active Enhancer Landscapes for Eliciting Transcription (RNA-Seq)

Enhancer activation is a critical step for gene activation. Here we report a novel epigenetic crosstalk at enhancers between the UTX (H3K27 demethylase)-MLL4 (H3K4 methyltransferase) complex and the histone acetyltransferase p300. We demonstrate that UTX, in a demethylase activity-independent manner, facilitates conversion of naïve (unmarked) enhancers in embryonic stem cells to an active (H3K4me1+/H3K27ac+) state by recruiting and coupling the enzymatic functions of MLL4 and p300. Loss of UTX leads to attenuated enhancer activity, characterized by reduced levels of H3K4me1 and H3K27ac as well as impaired transcription. The UTX-MLL4 complex enhances p300-dependent H3K27 acetylation through UTX-dependent stimulation of p300 recruitment while MLL4-mediated H3K4 monomethylation, reciprocally, requires p300 function. Importantly, MLL4-generated H3K4me1 further enhances p300-dependent transcription. This work reveals a previously unrecognized cooperativity among enhancer-associated chromatin modulators, including a unique function for UTX, in establishing an “active enhancer landscape” and defines a mechanism for the joint deposition of H3K4me1 and H3K27ac. RNA-sequencing of mouse ES cells.

增强子激活是基因激活的关键步骤。本研究报道了小鼠胚胎干细胞中UTX（组蛋白H3K27去甲基化酶）-MLL4（组蛋白H3K4甲基转移酶）复合物与组蛋白乙酰转移酶p300之间存在一种全新的增强子表观遗传串扰。我们证实，UTX可不依赖其去甲基化酶活性，通过招募并偶联MLL4与p300的酶促功能，促进胚胎干细胞中初始（未标记）增强子向激活态（H3K4me1+/H3K27ac+）转化。UTX缺失会导致增强子活性减弱，表现为H3K4me1与H3K27ac水平降低以及转录功能受损。UTX-MLL4复合物可通过UTX依赖性的p300招募，增强p300介导的H3K27乙酰化；而MLL4介导的H3K4单甲基化反过来也依赖p300的功能。尤为重要的是，MLL4产生的H3K4me1可进一步增强p300依赖的转录过程。本研究揭示了此前未被发现的增强子相关染色质调控因子之间的协同作用——其中包括UTX的独特功能——在构建“激活增强子图谱”中的作用，并阐明了H3K4me1与H3K27ac共同沉积的分子机制。本研究包含小鼠胚胎干细胞的RNA测序（RNA-sequencing）数据集。