Genome-wide mapping of histone H3K9me2 in acute myeloid leukemia reveals large chromosomal domains associated with massive gene silencing and sites of genome instability

A facultative heterochromatin mark, histone H3 lysine 9 dimethylation (H3K9me2), which is mediated by histone methyltransferases G9a/GLP (EHMT2/1), undergoes dramatic rearrangements during myeloid cell differentiation as observed by chromatin imaging. To determine whether these structural transitions also involve genomic repositioning of H3K9me2, we used ChIP-sequencing to map genome-wide topography of H3K9me2 in normal human granulocytes, normal CD34+ hematopoietic progenitors, primary myeloblasts from acute myeloid leukemia (AML) patients, and a model leukemia cell line K562. We observe that H3K9me2 naturally repositions from the previously designated “repressed” chromatin state in hematopoietic progenitors to predominant association with heterochromatin regions in granulocytes. In contrast, AML cells accumulate H3K9me2 on previously undefined large (> 100 Kb) genomic blocks that are enriched with AML-specific single nucleotide variants, sites of chromosomal translocations, and genes downregulated in AML. Specifically, the AML-specific H3K9me2 blocks are enriched with genes regulated by the proto-oncogene ERG that promotes stem cell characteristics. The AML-enriched H3K9me2 blocks (in contrast to the heterochromatin-associated H3K9me2 blocks enriched in granulocytes) are reduced by pharmacological inhibition of the histone methyltransferase G9a/GLP in K562 cells concomitantly with transcriptional activation of ERG and ETS1 oncogenes. Our data suggest that G9a/GLP mediate formation of transient H3K9me2 blocks that are preserved in AML myeloblasts and may lead to an increased rate of AML-specific mutagenesis and chromosomal translocations.

组蛋白H3赖氨酸9二甲基化（histone H3 lysine 9 dimethylation，H3K9me2）是一种兼性异染色质标记，由组蛋白甲基转移酶G9a/GLP（EHMT2/1）介导；通过染色质成像观察发现，其在髓系细胞分化过程中会发生显著重排。为明确此类结构转变是否同时伴随H3K9me2的基因组重定位，我们采用染色质免疫共沉淀测序（ChIP-sequencing）技术，对正常人类粒细胞、正常CD34阳性造血祖细胞、急性髓系白血病（AML）患者来源的原发性原幼髓系细胞，以及模型白血病细胞系K562中的H3K9me2全基因组分布图谱进行了绘制。研究观察到，H3K9me2会自然发生重定位：从造血祖细胞中原本定义为“沉默”的染色质状态，转向粒细胞中主要与异染色质区域结合的状态。与之相反，AML细胞会在此前未被标注的大型（>100 Kb）基因组结构域上富集H3K9me2；此类结构域富含AML特异性单核苷酸变异位点、染色体易位位点，以及在AML中表达下调的基因。具体而言，AML特异性H3K9me2结构域富集了受原癌基因ERG调控的基因——ERG可促进干细胞特性的维持。与粒细胞中富集于异染色质的H3K9me2结构域不同，AML中富集的H3K9me2结构域可通过在K562细胞中药物抑制组蛋白甲基转移酶G9a/GLP而减少，同时伴随原癌基因ERG与ETS1的转录激活。本研究数据表明，G9a/GLP介导形成的暂时性H3K9me2结构域会在AML原幼髓系细胞中得以保留，并可能提升AML特异性诱变与染色体易位的发生频率。