DNA Microarray-Based Genome-Wide Analyses of Plasmodium Parasites

DNA microarray is presently one of the most powerful and fastest growing technologies for genomic research of infectious diseases. Accordingly, DNA microarray-based global analyses of Plasmodium parasites provided many insights into the general biology of malaria infection. From the parasite perspective, it was shown that the complex Plasmodium life cycle is characterized by a high level of coordination in gene expression but at the same time parasites have a considerable capacity to alter their transcriptional profile as a response to external stimuli and/or adaptation to varying growth conditions in their host. In addition to transcriptional profiling, DNA microarrays were shown to be useful for quantitative analyses of Plasmodium genomic DNA including characterizations of sequence polymorphisms and copy number variants (CNV) as well as genomic loci associated with different chromatin factors (e.g., immunoprecipitated material (ChIP-on-chip)). Here, we present protocols for transcriptional profiling, comparative genomic hybridization (CGH), and ChIP-on-chip analyses that have been developed for the use of low-density long oligonucleotide DNA microarrays of Plasmodium species. Many of the presented procedures including RNA purification, DNA amplification, and chromatin immunoprecipitation are likely to be transferable to other genomic platforms such as other microarray technologies and new generation sequencing.