Simultaneous genome-wide gene expression and transcript isoform profiling in the human malaria parasite.
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 av...
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doaj-cd84398e913743f695b58f5cad1781742020-11-24T22:05:31ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-011211e018759510.1371/journal.pone.0187595Simultaneous genome-wide gene expression and transcript isoform profiling in the human malaria parasite.Lindsey B TurnbullGeoffrey H SiwoKatrina A Button-SimonsAsako TanLisa A CheckleyHeather J PainterManuel LlinásMichael T FerdigGene 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.http://europepmc.org/articles/PMC5675406?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Lindsey B Turnbull Geoffrey H Siwo Katrina A Button-Simons Asako Tan Lisa A Checkley Heather J Painter Manuel Llinás Michael T Ferdig |
spellingShingle |
Lindsey B Turnbull Geoffrey H Siwo Katrina A Button-Simons Asako Tan Lisa A Checkley Heather J Painter Manuel Llinás Michael T Ferdig Simultaneous genome-wide gene expression and transcript isoform profiling in the human malaria parasite. PLoS ONE |
author_facet |
Lindsey B Turnbull Geoffrey H Siwo Katrina A Button-Simons Asako Tan Lisa A Checkley Heather J Painter Manuel Llinás Michael T Ferdig |
author_sort |
Lindsey B Turnbull |
title |
Simultaneous genome-wide gene expression and transcript isoform profiling in the human malaria parasite. |
title_short |
Simultaneous genome-wide gene expression and transcript isoform profiling in the human malaria parasite. |
title_full |
Simultaneous genome-wide gene expression and transcript isoform profiling in the human malaria parasite. |
title_fullStr |
Simultaneous genome-wide gene expression and transcript isoform profiling in the human malaria parasite. |
title_full_unstemmed |
Simultaneous genome-wide gene expression and transcript isoform profiling in the human malaria parasite. |
title_sort |
simultaneous genome-wide gene expression and transcript isoform profiling in the human malaria parasite. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2017-01-01 |
description |
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. |
url |
http://europepmc.org/articles/PMC5675406?pdf=render |
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