Expression patterns of Plasmodium falciparum clonally variant genes at the onset of a blood infection in non-immune humans [ChIP-seq]

Clonally variant genes (CVGs) play fundamental roles in the adaptation of Plasmodium falciparum parasites to the fluctuating conditions of the human host, but their expression patterns under the natural conditions of the blood circulation have been characterized in detail only for a few specific gene families. Here we provide a detailed characterization of the full P. falciparum transcriptome across the full intraerythrocytic development cycle (IDC) at the onset of a blood infection in non-immune human volunteers. We found that the vast majority of transcriptional differences between parasites obtained from the volunteers and the parental parasite line maintained in culture occur for CVGs. Specifically, we observed a major increase in the transcript levels of most members of the pfmc-2tm and gbp families and of specific genes of other families, in addition to previously reported changes in var and clag3 genes. The expression patterns were almost identical between parasites obtained from the different volunteers. Large transcriptional differences correlate with changes in the distribution of histone modifications associated with heterochromatin, confirming their epigenetic nature. The analysis of parasites collected at different points along the infection indicates that when parasites pass through transmission stages, the epigenetic memory at CVG loci is lost, resulting in a reset of their expression state and reestablishment of new epigenetic patterns. Overall design: Samples from the NF54 parental line and V63 (parasites obtained from a volunteer who participated in a controlled human malaria infection trial) were processed to perform a ChIP-Seq experiment against H3K9me3.

克隆变异基因（Clonally variant genes, CVGs）在恶性疟原虫（Plasmodium falciparum）适应人类宿主内不断波动的微环境过程中发挥着核心作用，但目前仅针对少数特定基因家族，详细解析了其在血液循环自然条件下的表达模式。本研究针对非免疫人体志愿者血液感染初期的恶性疟原虫完整红细胞内发育周期（intraerythrocytic development cycle, IDC），完成了全转录组的系统表征。研究发现，从志愿者体内分离的疟原虫与体外培养的亲本疟原虫株之间的绝大多数转录差异，均发生在CVGs中。具体而言，除此前已报道的var与clag3基因表达变化外，pfmc-2tm家族、gbp家族的绝大多数成员以及其他家族的特定基因的转录水平均出现显著上调。不同志愿者体内分离的疟原虫，其基因表达模式几乎完全一致。大规模转录差异与异染色质相关组蛋白修饰的分布变化显著相关，证实了这些差异的表观遗传本质。对感染不同时间点采集的疟原虫进行分析后发现，当疟原虫经历传播阶段时，CVG位点的表观遗传记忆会丢失，进而导致其表达状态重置并建立全新的表观遗传模式。实验整体设计：对NF54亲本株与V63株（从参与可控性人类疟疾感染试验的志愿者体内分离的疟原虫）进行样本制备，开展针对H3K9me3的染色质免疫共沉淀测序（ChIP-Seq）实验。