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 ...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 m RNA 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.展开更多
基金supported by Eck Institute for Global Health Fellowshipssupported 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 Awardthe support from the Center for Quantitative Biology(P50 GM071508)。
文摘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 m RNA 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.
