Epigenomic Modifications Predict Active Promoters and Gene Structure in Toxoplasma gondii

Abstract

Mechanisms of gene regulation are poorly understood in Apicomplexa, a phylum that encompasses deadly human pathogens like Plasmodium and Toxoplasma. Initial studies suggest that epigenetic phenomena, including histone modifications and chromatin remodeling, have a profound effect upon gene expression and expression of virulence traits. Using the model organism Toxoplasma gondii, we characterized the epigenetic organization and transcription patterns of a contiguous 1% of the T. gondii genome using custom oligonucleotide microarrays. We show that methylation and acetylation of histones H3 and H4 are landmarks of active promoters in T. gondii that allow us to deduce the position and directionality of gene promoters with >95% accuracy. These histone methylation and acetylation “activation” marks are strongly associated with gene expression. We also demonstrate that the pattern of histone H3 arginine methylation distinguishes certain promoters, illustrating the complexity of the histone modification machinery in Toxoplasma. By integrating epigenetic data, gene prediction analysis, and gene expression data from the tachyzoite stage, we illustrate feasibility of creating an epigenomic map of T. gondii tachyzoite gene expression. Further, we illustrate the utility of the epigenomic map to empirically and biologically annotate the genome and show that this approach enables identification of previously unknown genes. Thus, our epigenomics approach provides novel insights into regulation of gene expression in the Apicomplexa. In addition, with its compact genome, genetic tractability, and discrete life cycle stages, T. gondii provides an important new model to study the evolutionarily conserved components of the histone code.

Toxoplasma gondiigene expression is under the control of regulatory pathways acting through chromatin structure

“…The biological meaning of this observation is still unknown but it was found that deacetylated histone-containing sites are associated with a reduced level of expression of the neighboring genes, suggesting a polar effect of these epigenetic modifications on the surrounding genes (e.g. bradyzoite-specific BSR4-related genes, Saksouk et al, 2005;Gissot et al, 2007). Thus, several coexpressed genes are clustered into eu-or heterochromatin domains, which suggest that chromatin, can be further divided into separate domains.…”

“…1). Besides, some of these marks on histone have been shown to have evolutionarily conserved roles in transcription regulation (Saksouk et al, 2005;Sullivan & Hakimi, 2006;Gissot et al, 2007). Physical maps describing the exact position of each modified histone on the genome provides an invaluable tool to analyze its complex regulatory circuits involved in the gene expression.…”

“…1B). Moreover, long-range histone acetylation patterns spanning many kilobases contribute to coordinate transcription of stage-specific tandemly arrayed multigene clusters (Saksouk et al, 2005;Gissot et al, 2007). In heterochromatin, the transcription of genes is usually repressed, whereas genes in euchromatin are usually active.…”

“…This mechanism may facilitate the coregulation of large subset of genes during differentiation or other cell processes. In addition to histone acetylation, H3R17me2 and H3K4me3 methylations have been attributed to parasite gene activation (Saksouk et al, 2005;Gissot et al, 2007;Fig. 1B).…”

“…city of chromatin immunoprecipitation with the unbiased, high-throughput capabilities of microarrays (ChIPon-chip; Robyr et al, 2002). Applied to T. gondii, ChIP-on-chip analyses [genome-wide (Sautel et al, 2007) or on a tiling arrays encompassing a 0.65-Mb contiguous portion of the chromosome 1b (Gissot et al, 2007)] reveal that several modifications co-localize at precise loci and correlate either with significant gene expression or gene silencing. In the same manner as mentioned above, we observed at certain loci, that contiguous sets of genes were coregulated.…”