The cryptic unstable transcripts are associated with developmentally regulated gene expression in blood-stage Plasmodium falciparum

The tight gene expression regulation controls the development and pathogenesis of human malaria parasite Plasmodium falciparum throughout the complex life cycle. Recent studies have revealed the pervasive nascent transcripts in the genome of P. falciparum, suggesting the existence of a hidden transcriptome involved in the dynamic gene expression. However, the landscape and related biological functions of nascent non-coding RNAs (ns-ncRNAs) are still poorly explored. Here we profiled the transcription dynamics of nascent RNAs by rRNA-depleted and stranded RNA sequencing over the course of 48-h intraerythrocytic developmental cycle (IDC). We identified the genome-wide sources of a total of 2252 ns-ncRNAs, mostly originating from intergenic and untranslated regions of annotated genes. By integrating the nascent RNA abundances with ATAC-seq and ChIP-seq analysis, we uncovered the euchromatic microenvironment surrounding the ns-ncRNA loci, and revealed a positive correlation between ns-ncRNAs and corresponding mRNA abundances. Finally, by gene knock-down strategy, we showed that the cooperation of RNA exosome catalytic subunit PfDis3 and PfMtr4 cofactor played a major role in ns-ncRNAs degradation. Collectively, this study contributes to understanding of the potential roles of short-lived nascent ncRNAs in regulating gene expression in malaria parasites.

严谨的基因表达调控，贯穿人类疟疾寄生虫恶性疟原虫（Plasmodium falciparum）复杂的生命周期，调控其发育与致病进程。已有研究在恶性疟原虫基因组中发现了广泛分布的新生转录本，提示存在一类参与动态基因表达调控的隐秘转录组。然而，新生非编码RNA（nascent non-coding RNAs, ns-ncRNAs）的转录全景及其相关生物学功能，目前仍未得到充分探究。本研究通过核糖体RNA消减链特异性RNA测序技术，对恶性疟原虫48小时红细胞内发育周期（intraerythrocytic developmental cycle, IDC）全程的新生RNA转录动态进行了全景分析。本研究在全基因组范围内共鉴定出2252个ns-ncRNAs，其中大多数源自注释基因的基因间区与非翻译区。通过将新生RNA表达水平与转座酶可及性染色质测序（ATAC-seq）、染色质免疫沉淀测序（ChIP-seq）分析结果整合，我们揭示了ns-ncRNA基因座周围的常染色质微环境，并发现ns-ncRNAs与其对应的mRNA表达量呈正相关。最后，通过基因敲低实验策略，我们证实RNA外切体催化亚基PfDis3与辅助因子PfMtr4的协同作用，在ns-ncRNAs的降解过程中发挥了关键作用。综上，本研究有助于加深对短命新生非编码RNA在疟疾寄生虫基因表达调控中潜在功能的理解。