Screening of differentially expressed genes in three Plasmodium falciparum parasite lines [RNA-seq]

We performed RNA-Seq analysis with synchronized 0-6h ring stage parasites of three P.falciparum lines within their third life cycle, to study the change of expression profiling when knocking down PfSWIB. The comparison analysis on screening of differentially expressed genes was done in parasite lines including 3D7(wild type: blank control), PfSWIB (wild type: self-control) and PfSWIB? (PfSWIB knockdown). Approximately 10.8% of the transcripts showed up-regulation between the PfSWIB-KD and two WT parasite, whereas 11.9% showed down-regulation (Fold change>1.5, P<0.05). Hierarchical clustering of differentially expressed genes uncovered several transcription factors such as PfApiAP2 family and PfSir2B, as well as certain histone modification enzymes, which proved to be involved in regulating on var gene transcription. We further screened out a number of var genes which exhibited differential expression among different lines, and performed qPCR on 44 di?erentially expressed vars in the PfSWIB vs PfSWIB? comparison group based on the RNA-seq results, to study the transcription patterns of upsA-, upsB- and upsC-subtype var genes. We found that most upsA- and upsC- type vars were significant down-regulated in PfSWIB? line. In contrast, the expression pattern of partial upsB vars presented a distinct change in PfSWIB? line. The RNA-seq and qPCR analysis provide a better understanding of the mechanism and function of PfSWIB on regulating the expression switching and clonal variation of var gene family contributing to the pathogenesis in malaria parasites. Overall design: Examination of gene expression changes in 3 P.falciparum parasite lines including 3D7(wide type), PfSWIB(self-control) and PfSWIB?(knock down).