Transcriptomics

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


ABSTRACT: 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.

ORGANISM(S): Plasmodium falciparum

PROVIDER: GSE221211 | GEO | 2023/02/08

REPOSITORIES: GEO

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