GSE104347
Genome-wide localisation of histone variants in Toxoplasma gondii implicates variant exchange in transcriptional control by demarcation of functional chromatin regions (ChIP-seq)
Chromatin is composed of DNA wrapped around nucleosomes, complexes consisting of highly basic proteins called histones. Histone variants are non-canonical variants of histones that have specific functions. The Apicomplexan parasite Toxoplasma gondii possesses conserved histone variants CenH3, H3.3, H2A.Z, H2A.X, as well as the parasite-specific H2B variant, H2BV (or H2B.Z). We surveyed the genome-wide distribution of T. gondii histone variants by chromatin immunoprecipitation coupled with microarray (ChIP-chip) and next generation sequencing (ChIP-seq). Histone variants have specific localisations in chromosomes and in relation to genomic features. Histones H2BV and H2AZ localise to promoter regions with the transcriptional activation mark H3K4me3. Sites where H2BV, H2AZ and H3K4me3 colocalise are enriched in motifs recognised by AP2 transcription factors, particularly in the nucleosome-free region just upstream of the transcription start site. In contrast, histone variants H3.3 and H2AX are largely absent from promoters but enriched in gene bodies. Consistent with previous biochemical work, the majority of H2AX and H2AZ loci do not overlap, suggesting that they are present in different nucleosomes. In addition, the T. gondii homologue of the centromeric histone CenH3 demarcates centromeric chromatin and appears to be part of a unique centromeric histone complex including H3.3 that localises to centromeric chromatin as detected in proteomic analysis of co-immunoprecipitated CenH3 complexes. Together, these data suggest that the position of variant histones demarcates specific functional regions of chromatin and that exchange of histone variants is an important transcriptional regulatory mechanism in T. gondii. Overall design: Localization of histone variants in Toxoplasma gondii by ChIP-chip and ChIP-seq