Destabilization of chromosome structure by histone H3 lysine 27 methylation
Destabilization of chromosome structure by histone H3 lysine 27 methylation
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DOI：
10.1371/journal.pgen.1008093
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发表时间：
2019-04-01
期刊：
影响因子：
4.5
通讯作者：
Stukenbrock, Eva H.
中科院分区：
文献类型：
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作者：
Moeller, Mareike;Schotanus, Klaas;Stukenbrock, Eva H.
染色体和基因组的稳定性对正常细胞功能至关重要，因为不稳定性往往与疾病和DNA修复机制的功能障碍有关。许多生物体保持着偏离标准染色体的额外或辅助染色体。致病性真菌酵母（Zymoseptoria tritici）有多达8条副染色体，在减数分裂和有丝分裂过程中高度不稳定，转录受到抑制，重复元件富集，并富集异色组蛋白甲基化标记，如H3赖氨酸9或赖氨酸27 （H3K9me3, H3K27me3）的三甲基化。为了阐明异染色质对小麦小麦基因组稳定性的作用，我们分别删除了编码H3K9me3和H3K27me3、kmt1和kmt6的甲基转移酶基因，并产生了一个双突变体。我们结合实验进化和基因组分析来确定这些缺失对染色体和基因组稳定性的影响，无论是在体外还是在植物中。我们使用全基因组测序、ChIP-seq和RNA-seq来比较突变型和野生型菌株的基因组和染色质结构的变化以及基因表达的差异。对H3K9me3缺陷菌株的基因组和ChIP-seq数据分析显示，H3K27me3在野生型中大部分被重新定位到富含H3K9me3的区域。在缺乏H3K9me3的情况下，发现了许多基因组重排和新染色体的形成，并伴随着转座因子的激活。与之形成鲜明对比的是，在体外正常生长条件下，H3K27me3的缺失实际上增加了辅助染色体的稳定性，即使基因活性没有大规模变化。我们得出结论，H3K9me3对维持基因组稳定性很重要，因为它不允许H3K27me3进入被认为是组成性异染色质的区域。在这个系统中，H3K27me3降低了辅助染色体的整体稳定性，使这些基因组的准必需区域产生亚稳态。基因组和染色体的稳定性是维持正常细胞功能和活力的必要条件。然而，基因组和染色体结构的差异经常出现在对不断变化的环境条件进行快速适应的生物体中，在人类中也经常出现在癌细胞中。我们研究基因组的不稳定性在真菌病原体，表现出高度的遗传多样性。在这种病原体中表现出非凡多样性的区域是富含转座子的辅助染色体，其中包含很少的基因，这些基因对生物体有未知的益处，但在群体中维持，因此被认为是准必需的。目前所研究的所有真菌的辅助染色体都富含异染色质标记，即H3赖氨酸9和27的三甲基化（H3K9me3, H3K27me3）。我们发现这些异染色质标记的丢失对基因组稳定性有强烈但相反的影响。虽然转座子相关标记H3K9me3的缺失会破坏整个基因组的稳定性，但H3K27me3的存在有利于辅助染色体的不稳定性。我们的研究为染色质和基因组稳定性之间的关系以及为什么一些区域比其他区域更容易受到遗传多样性的影响提供了见解。
Chromosome and genome stability are important for normal cell function as instability often correlates with disease and dysfunction of DNA repair mechanisms. Many organisms maintain supernumerary or accessory chromosomes that deviate from standard chromosomes. The pathogenic fungus Zymoseptoria tritici has as many as eight accessory chromosomes, which are highly unstable during meiosis and mitosis, transcriptionally repressed, show enrichment of repetitive elements, and enrichment with heterochromatic histone methylation marks, e.g., trimethylation of H3 lysine 9 or lysine 27 (H3K9me3, H3K27me3). To elucidate the role of heterochromatin on genome stability in Z. tritici, we deleted the genes encoding the methyltransferases responsible for H3K9me3 and H3K27me3, kmt1 and kmt6, respectively, and generated a double mutant. We combined experimental evolution and genomic analyses to determine the impact of these deletions on chromosome and genome stability, both in vitro and in planta. We used whole genome sequencing, ChIP-seq, and RNA-seq to compare changes in genome and chromatin structure, and differences in gene expression between mutant and wildtype strains. Analyses of genome and ChIP-seq data in H3K9me3-deficient strains revealed dramatic chromatin reorganization, where H3K27me3 is mostly relocalized into regions that are enriched with H3K9me3 in wild type. Many genome rearrangements and formation of new chromosomes were found in the absence of H3K9me3, accompanied by activation of transposable elements. In stark contrast, loss of H3K27me3 actually increased the stability of accessory chromosomes under normal growth conditions in vitro, even without large scale changes in gene activity. We conclude that H3K9me3 is important for the maintenance of genome stability because it disallows H3K27me3 in regions considered constitutive heterochromatin. In this system, H3K27me3 reduces the overall stability of accessory chromosomes, generating a metastable state for these quasi-essential regions of the genome.Author summary Genome and chromosome stability are essential to maintain normal cell function and viability. However, differences in genome and chromosome structure are frequently found in organisms that undergo rapid adaptation to changing environmental conditions, and in humans are often found in cancer cells. We study genome instability in a fungal pathogen that exhibits a high degree of genetic diversity. Regions that show extraordinary diversity in this pathogen are the transposon-rich accessory chromosomes, which contain few genes that are of unknown benefit to the organism but maintained in the population and thus considered quasi-essential. Accessory chromosomes in all fungi studied so far are enriched with markers for heterochromatin, namely trimethylation of H3 lysine 9 and 27 (H3K9me3, H3K27me3). We show that loss of these heterochromatin marks has strong but opposing effects on genome stability. While loss of the transposon-associated mark H3K9me3 destabilizes the entire genome, presence of H3K27me3 favors instability of accessory chromosomes. Our study provides insight into the relationship between chromatin and genome stability and why some regions are more susceptible to genetic diversity than others.