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

• DOI: 10.1371/journal.pone.0187595
• Publication Date: 2017-11-07T22:04:17Z
• Authors: Lindsey B. Turnbull; Geoffrey H. Siwo; Katrina A. Button...; Asako Tan; Lisa A. Checkley; Heather J. Painter; Manuel Llinás; Michael T. Ferdig
• Keywords: 0301 basic medicine; Plasmodium; Science; Q; R; Gene Expression; Exons; 3. Good health; Alternative Splicing; 03 medical and health sciences; Medicine; Animals; Humans; RNA, Messenger; Research Article; Oligonucleotide Array Sequence Analysis

Gene expression DNA microarrays have been vital for characterizing whole-genome transcriptional profiles. Nevertheless, their effectiveness relies heavily on the accuracy of genome sequences, the annotation of gene structures, and the sequence-dependent performance of individual probes. Currently available gene expression arrays for the malaria parasite Plasmodium falciparum rely on an average of 2 probes per gene, usually positioned near the 3' end of genes; consequently, existing designs are prone to measurement bias and cannot capture complexities such as the occurrence of transcript isoforms arising from alternative splicing or alternative start/ stop sites. Here, we describe two novel gene expression arrays with exon-focused probes designed with an average of 12 and 20 probes spanning each gene. This high probe density minimizes signal noise inherent in probe-to-probe sequence-dependent hybridization intensity. We demonstrate that these exon arrays accurately profile genome-wide expression, comparing favorably to currently available arrays and RNA-seq profiling, and can detect alternatively spliced transcript isoforms as well as non-coding RNAs (ncRNAs). Of the 964 candidate alternate splicing events from published RNA-seq studies, 162 are confirmed using the exon array. Furthermore, the exon array predicted 330 previously unidentified alternate splicing events. Gene expression microarrays continue to offer a cost-effective alternative to RNA-seq for the simultaneous monitoring of gene expression and alternative splicing events. Microarrays may even be preferred in some cases due to their affordability and the rapid turn-around of results when hundreds of samples are required for fine-scale systems biology investigations, including the monitoring of the networks of gene co-expression in the emergence of drug resistance.