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Inhibition of DNA Methylation in Picochlorum soloecismus Alters Algae Productivity
Frontiers in Genetics ( IF 3.7 ) Pub Date : 2020-09-03 , DOI: 10.3389/fgene.2020.560444
Christina R. Steadman , Shounak Banerjee , Yuliya A. Kunde , Claire K. Sanders , Babetta L. Marrone , Scott N. Twary

Eukaryotic organisms regulate the organization, structure, and accessibility of their genomes through chromatin remodeling that can be inherited as epigenetic modifications. These DNA and histone protein modifications are ultimately responsible for an organism’s molecular adaptation to the environment, resulting in distinctive phenotypes. Epigenetic manipulation of algae holds yet untapped potential for the optimization of biofuel production and bioproduct formation; however, epigenetic machinery and modes-of-action have not been well characterized in algae. We sought to determine the extent to which the biofuel platform species Picochlorum soloecismus utilizes DNA methylation to regulate its genome. We found candidate genes with domains for DNA methylation in the P. soloecismus genome. Whole-genome bisulfite sequencing revealed DNA methylation in all three cytosine contexts (CpG, CHH, and CHG). While global DNA methylation is low overall (∼1.15%), it occurs in appreciable quantities (12.1%) in CpG dinucleotides in a bimodal distribution in all genomic contexts, though terminators contain the greatest number of CpG sites per kilobase. The P. soloecismus genome becomes hypomethylated during the growth cycle in response to nitrogen starvation. Algae cultures were treated daily across the growth cycle with 20 μM 5-aza-2′-deoxycytidine (5AZA) to inhibit propagation of DNA methylation in daughter cells. 5AZA treatment significantly increased optical density and forward and side scatter of cells across the growth cycle (16 days). This increase in cell size and complexity correlated with a significant increase (∼66%) in lipid accumulation. Site specific CpG DNA methylation was significantly altered with 5AZA treatment over the time course, though nitrogen starvation itself induced significant hypomethylation in CpG contexts. Genes involved in several biological processes, including fatty acid synthesis, had altered methylation ratios in response to 5AZA; we hypothesize that these changes are potentially responsible for the phenotype of early induction of carbon storage as lipids. This is the first report to utilize epigenetic manipulation strategies to alter algal physiology and phenotype. Collectively, these data suggest these strategies can be utilized to fine-tune metabolic responses, alter growth, and enhance environmental adaption of microalgae for desired outcomes.



中文翻译:

苦竹中DNA甲基化的抑制改变藻类生产力

真核生物通过染色质重塑来调节其基因组的组织,结构和可及性,染色质重塑可以作为表观遗传修饰而遗传。这些DNA和组蛋白的修饰最终负责生物体对环境的分子适应,从而导致独特的表型。藻类的表观遗传操纵在优化生物燃料生产和生物产品形成方面具有尚未开发的潜力;然而,在藻类中表观遗传机制和作用方式尚未得到很好的表征。我们试图确定生物燃料平台物种的程度苦瓜利用DNA甲基化来调节其基因组。我们发现了具有DNA甲基化结构域的候选基因梭子蟹基因组。全基因组亚硫酸氢盐测序揭示了在所有三个胞嘧啶环境(CpG,CHH和CHG)中的DNA甲基化。尽管总体DNA甲基化总体较低(〜1.15%),但在所有基因组背景下,CpG二核苷酸中的双峰分布都以可观的数量(12.1%)发生,尽管终止子每千碱基的CpG位点数量最多。的梭子蟹基因组在生长周期中因缺氮而甲基化不足。在整个生长周期中,每天用20μM5-氮杂2'-脱氧胞苷(5AZA)处理藻类培养物,以抑制子代细胞中DNA甲基化的传播。5AZA处理显着增加了整个生长周期(16天)的光密度以及细胞的前向和侧向散射。细胞大小和复杂性的增加与脂质积累的显着增加(约66%)相关。尽管氮饥饿本身在CpG环境中引起明显的低甲基化,但在5AZA处理过程中,位点特异性CpG DNA甲基化发生了显着变化。涉及脂肪酸合成等几个生物过程的基因已经改变了对5AZA的甲基化率。我们假设这些变化可能是导致碳存储作为脂质早期诱导的表型的原因。这是第一个利用表观遗传操纵策略改变藻类生理和表型的报告。总体而言,这些数据表明这些策略可用于微调代谢反应,改变生长并增强微藻对所需结果的环境适应性。

更新日期:2020-10-16
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