Genome wide distribution of G-quadruplexes and their impact on gene expression in malaria parasites
Genome wide distribution of G-quadruplexes and their impact on gene expression in malaria parasites
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DOI：
10.1371/journal.pgen.1008917
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发表时间：
2020-07-01
期刊：
影响因子：
4.5
通讯作者：
Lopez-Rubio, Jose-Juan
中科院分区：
文献类型：
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作者：
Gazanion, Elodie;Lacroix, Laurent;Lopez-Rubio, Jose-Juan
疟疾寄生虫的转录控制机制尚未完全了解。 G-四链体 (G4) DNA 基序在寄生虫富含 AT 的基因组中的定位模式，特别是在编码毒力因子的 vargene 家族中，以及在重组热点附近，表明 G4 在基因表达和基因组稳定性中可能具有调节作用。在这里，我们使用 G4Hunter 对恶性疟原虫基因组中的 G4 进行了迄今为止最全面的全基因组调查，该调查考虑到 G 丰富度和 G 偏度来识别 G4 形成序列 (G4FS)。我们展示了 G4FS 在核小体耗尽区域和 Vargenes 第一个外显子中的富集，这种模式在密切相关的紫菜疟原虫寄生虫中是保守的。在 G4 稳定条件下，即用吡啶他汀（一种高亲和力 G4 配体）处理后，我们发现在 var 启动子的非编码链中发现的真正的 G4 调节报告基因表达。此外，吡啶他汀处理的寄生虫的转录谱显示出大规模的扰动，其中失调会影响转录因子的 ApiAP2 家族和参与核糖体生物发生的基因。总体而言，我们的研究强调 G4 作为重要的 DNA 二级结构，在疟原虫基因表达调控、亚端粒重组和变异基因生物学中发挥作用。作者摘要 疟疾持续成为全球健康问题，是由不同的疟原虫属真核寄生虫引起的。这些寄生虫具有复杂的生命周期，在此期间阶段转换的特点是受到严格调控的级联，以确保特定阶段的基因表达，但目前尚未完全了解。在这里，我们使用 G4Hunter 对寄生虫富含 AT 的基因组中的 G 四链体 (G4) DNA 基序进行了全基因组扫描。我们强调了核小体耗尽区域和vargenes第一个外显子中G4的显着富集，它们编码与严重疟疾相关的重要毒力因子。这是拉维尼亚亚属疟原虫相关物种中保守的模式。然后，我们使用荧光素酶报告系统验证 G4 对转录的调节功能。最后，我们发现高选择性 G4 稳定配体吡啶他汀会引起恶性疟原虫转录组的大规模扰动，从而展示其作为抗疟药的潜力。总而言之，我们的研究强调 G4 作为疟原虫基因调控的新层，并且可能是 vargene 多样性的增强剂。
Mechanisms of transcriptional control in malaria parasites are still not fully understood. The positioning patterns of G-quadruplex (G4) DNA motifs in the parasite's AT-rich genome, especially within thevargene family which encodes virulence factors, and in the vicinity of recombination hotspots, points towards a possible regulatory role of G4 in gene expression and genome stability. Here, we carried out the most comprehensive genome-wide survey, to date, of G4s in thePlasmodium falciparumgenome using G4Hunter, which identifies G4 forming sequences (G4FS) considering their G-richness and G-skewness. We show an enrichment of G4FS in nucleosome-depleted regions and in the first exon ofvargenes, a pattern that is conserved within the closely relatedLaverania Plasmodiumparasites. Under G4-stabilizing conditions,i.e., following treatment with pyridostatin (a high affinity G4 ligand), we show that abona fideG4 found in the non-coding strand ofvarpromoters modulates reporter gene expression. Furthermore, transcriptional profiling of pyridostatin-treated parasites, shows large scale perturbations, with deregulation affecting for instance the ApiAP2 family of transcription factors and genes involved in ribosome biogenesis. Overall, our study highlights G4s as important DNA secondary structures with a role inPlasmodiumgene expression regulation, sub-telomeric recombination andvargene biology.Author summary Malaria persists as a global health concern and is caused by divergent eukaryotic parasites of the genusPlasmodium. These parasites have a complex life cycle during which stage transitions are characterised by tightly regulated cascades that ensure stage-specific gene expression, which are not yet fully understood. Here, we have performed a genome wide scan of G-quadruplex (G4) DNA motifs in the parasite's AT-rich genome, using G4Hunter. We highlight a significant enrichment of G4s in nucleosome-depleted regions and in the first exon ofvargenes, which encode an important virulence factor associated with severe malaria. This is a pattern conserved amongPlasmodium-related species of theLaveraniasubgenus. We then validate the regulatory function of G4s on transcription, using a luciferase reporter system. Finally, we show that the highly selective G4-stabilizing ligand pyridostatin causes large scale perturbations of the transcriptome inPlasmodium falciparum, thus showcasing their potential as antimalarials. Altogether, our study highlights G4s as a new layer of gene regulation in malaria parasites, and a likely potentiator ofvargene diversity.