Analysis of Differentially Expressed Parasite Genes and Proteins Using Transcriptomics and Proteomics
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At any particular point in time, the full complement of transcribed RNAs and relevant proteins of a cell are known as the transcriptome and proteome, respectively. The composition of these two populations changes throughout the life cycle of a parasite or in response to environmental factors, such as drug treatments. Comparing the changes in the composition of the transcriptome and proteome between different life-cycle stages or in the same stage but under different conditions can be of particular interest, as it can allow the identification of potentially important differentially expressed genes and proteins. Combining the analysis of both the transcriptome and proteome in tandem allows changes in RNA transcripts to be followed right through to changes in the level of protein expression.
The protocols in this chapter describe methods for analyzing the transcriptome, by using suppression subtraction hybridization to construct subtracted complementary DNA libraries, and the proteome, by using two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis. These two methods are then integrated to allow the global changes in RNA and protein expression to be examined. The protocols have been adapted for working on parasites and contain extensive notes.
