HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia [763_ChIP-seq]

Although originally described as transcriptional activator, SPI1/PU.1, a major player in haematopoiesis whose alterations are associated with haematological malignancies, has the ability to repress transcription. Here, we investigated the mechanisms underlying gene repression in the erythroid lineage, in which SPI1 exerts an oncogenic function by blocking differentiation. We show that SPI1 represses genes by binding active enhancers that are located in intergenic or gene body regions. HDAC1 acts as a cooperative mediator of SPI1-induced transcriptional repression by deacetylating SPI1-bound enhancers in a subset of genes, including those involved in erythroid differentiation. Enhancer deacetylation impacts on promoter acetylation, chromatin accessibility and RNA pol II occupancy. In addition to the activities of HDAC1, polycomb repressive complex 2 (PRC2) reinforces gene repression by depositing H3K27me3 at promoter sequences when SPI1 is located at enhancer sequences. Moreover, our study identified a synergistic relationship between PRC2 and HDAC1 complexes in mediating the transcriptional repression activity of SPI1, ultimately inducing synergistic adverse effects on leukaemic cell survival. Our results highlight the importance of the mechanism underlying transcriptional repression in leukemic cells, involving complex functional connections between SPI1 and the epigenetic regulators PRC2 and HDAC1. Overall design: Genome-wide maps of SPI1, RNApolII and H3K4me1, H3K27ac, H3K27me3 in TgSpi1 erythroleukemic cells (#763) overexpressing SPI1 or not (dox inducible shRNA anti-Spi1) or treated with Entinostat or DMSO. Please note that the *rep1-2.bed/bw data is linked to the corresponding *rep1 sample records.

尽管SPI1/PU.1最初被认定为转录激活因子，但其却是造血调控的核心因子之一，自身异常与血液系统恶性肿瘤密切相关，且具备转录抑制能力。本研究针对红系谱系中SPI1介导的基因抑制机制展开探究——在该谱系中，SPI1通过阻断细胞分化发挥致癌功能。研究发现，SPI1可通过结合位于基因间区或基因本体区域的活性增强子，实现对靶基因的转录抑制。在部分靶基因（涵盖参与红系分化的基因）中，组蛋白去乙酰化酶1（HDAC1）可通过去乙酰化SPI1结合的增强子，作为SPI1诱导转录抑制的协同介导因子发挥作用。增强子去乙酰化会影响启动子乙酰化水平、染色质开放状态以及RNA聚合酶II（RNA pol II）的结合占有率。除HDAC1的调控作用外，多梳抑制复合体2（PRC2）可在SPI1结合增强子时，通过在启动子区域沉积H3K27me3修饰，进一步强化基因抑制效应。此外，本研究还发现PRC2与HDAC1复合体在介导SPI1的转录抑制活性时存在协同关系，最终协同抑制白血病细胞的存活。本研究结果凸显了白血病细胞中转录抑制机制的重要性，该机制涉及SPI1与表观遗传调控因子PRC2和HDAC1之间复杂的功能互作。实验整体设计：在过表达SPI1或未过表达SPI1（采用多西环素诱导的抗SPI1短发夹RNA（shRNA）进行干预）的TgSpi1红白血病细胞（#763）中，以及经恩替诺特（Entinostat）或二甲基亚砜（DMSO）处理的该类细胞中，获取SPI1、RNA pol II以及组蛋白修饰H3K4me1、H3K27ac、H3K27me3的全基因组结合图谱。请注意：*rep1-2.bed/bw格式的数据与对应的*rep1样本记录相关联。