Transcriptome of ring-stage parasites responses to stress conditions upon knockdown of PfGCN5

Purpose: this study is to analyze the change of overal transcriptome after three stress conditions in ring-stage Plasmodium falciparum before and after knockdown of PfGCN5 by TetR-DOZI system. Methods: In this study, the transcriptomes of a parasite line (TetR-PfGCN5::GFP) for knockdown (KD) of PfGCN5 by withdral of anhydrotetracycline (aTc) comparing to its control (TetR-PfGCN5::GFP with aTc) under three stress conditions [HS: heat shock, low-glucose starvation: L-Glu, and low dose of dihydroartemisinin (DHA) treatment] were analyzed at ring stage by RNAseq. Total RNA were harvested from the eary ring stages after 6 h of stress conditions using the Quick-RNA MiniPrep kit (Zymo Research). RNA sequencing libraries were prepared using the KAPA stranded RNA-seq library preparation kit (Roche) with 500 ng RNA from each sample. Illumina adapter sequence removal and quality trimming of reads were performed using Trimmomatic. Only reads that had a minimum length of 50 base pairs were retained. Reads were then mapped to the P. falciparum 3D7 strain reference genome with HISAT2. Results: Using an optimized data analysis workflow, we mapped about 5 million sequence reads per sample to the malaria parasite genome (pf3D7_V3.0.) and identified over 5 thousands transcripts with high mapping rate at the range between 80% and 95. PfGCN5 KD profoundly changed the global transcription pattern upon stress conditions, indicating PfGCN5 is involved in stress responses. Conclusions: Collectively, transcriptomic analysis of PfGCN5-dependent stress responses shows PfPfGCN5 plays important role in gene regulation of stress responses. mRNA profiles of TetR-PfGCN5::GFP with aTc, TetR-PfGCN5::GFP without aTc under three stress conditions (HS, L-Glu and DHA) were generated by deep sequencing, in two or three replicates