Sources of transcription variation in <i>Plasmodium falciparum</i>

Lindsey B. Turnbull; Katrina A. Button-Simons; Nestor Agbayani; Michael T. Ferdig

doi:10.1016/j.jgg.2022.03.008

Volume 49 Issue 10

Oct. 2022

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Article Navigation > Journal of Genetics and Genomics > 2022 > 49(10): 965-974

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Sources of transcription variation in Plasmodium falciparum

doi: 10.1016/j.jgg.2022.03.008

a. Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
b. Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA;
c. Rush School of Medicine, Chicago, IL 60612, USA

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Lindsey B. Turnbull and Katrina A. Button-Simons were supported by Eck Institute for Global Health Fellowships. This work was supported by the Indiana Clinical and Translational Sciences Institute (UL1TR001108) from the National Institutes of Health, National Center for Advancing Translational Sciences, Clinical and Translational Sciences Award and with the support from the Center for Quantitative Biology (P50 GM071508). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Received Date: 2021-11-18
Accepted Date: 2022-03-22
Rev Recd Date: 2022-03-21
Publish Date: 2022-04-06

Abstract

Abstract

Variation in transcript abundance can contribute to both short-term environmental response and long-term evolutionary adaptation. Most studies are designed to assess differences in mean transcription levels and do not consider other potentially important and confounding sources of transcriptional variation. Detailed quantification of variation sources will improve our ability to detect and identify the mechanisms that contribute to genome-wide transcription changes that underpin adaptive responses. To quantify innate levels of expression variation, we measured mRNA levels for more than 5000 genes in the malaria parasite, Plasmodium falciparum, among clones derived from two parasite strains across biologically and experimentally replicated batches. Using a mixed effects model, we partitioned the total variation among four sources—between strain, within strain, environmental batch effects, and stochastic noise. We found 646 genes with significant variation attributable to at least one of these sources. These genes were categorized by their predominant variation source and further examined using gene ontology enrichment analysis to associate function with each source of variation. Genes with environmental batch effect and within strain transcript variation may contribute to phenotypic plasticity, while genes with between strain variation may contribute to adaptive responses and processes that lead to parasite strain-specific survival under varied conditions.
- Expression variation,
- Malaria,
- Transcription,
- Cloning,
- Microarray

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References(44)

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