Simultaneous genome-wide gene expression and transcript isoform profiling in the human malaria parasite

Area of Science:

• Genomics
• Molecular Biology
• Parasitology

Background:

• Gene expression DNA microarrays are crucial for transcriptional profiling but face limitations with current Plasmodium falciparum arrays.
• Existing arrays use few probes per gene, leading to measurement bias and inability to detect transcript complexity like alternative splicing.

Purpose of the Study:

• To develop and validate novel exon-focused DNA microarrays for Plasmodium falciparum with high probe density.
• To assess the accuracy of these arrays in profiling genome-wide expression and detecting alternative splicing and non-coding RNAs.

Main Methods:

• Design of two novel gene expression arrays with an average of 12 and 20 exon-focused probes per gene.
• Comparison of array performance against existing arrays and RNA-sequencing (RNA-seq) profiling.
• Analysis of confirmed and predicted alternative splicing events and detection of non-coding RNAs.

Main Results:

• The novel exon arrays provide accurate genome-wide expression profiling, outperforming current arrays.
• These arrays successfully detected alternatively spliced transcript isoforms and non-coding RNAs.
• 162 out of 964 candidate alternative splicing events were confirmed, and 330 novel events were predicted.

Conclusions:

• High-density exon arrays offer a cost-effective and accurate method for monitoring gene expression and alternative splicing in Plasmodium falciparum.
• Microarrays remain a valuable tool, potentially preferred over RNA-seq for large-scale systems biology studies due to affordability and speed.
• These arrays can aid in understanding gene co-expression networks relevant to drug resistance emergence in malaria parasites.