Toxoplasma gondii is an obligate intracellular parasite. Toxoplasmosis is 
incurable because of its ability to differentiate from the rapidly replicating 
tachyzoite stage into a latent cyst form (bradyzoite stage). Gene regulation 
pertinent to Toxoplasma differentiation involves histone modification, but very 
little is known about the histone proteins in this early branching eukaryote. 
Here, we report the characterization of three H2A histones, variants H2AX and 
H2AZ, and a canonical H2A1. H2AZ is the minor parasite H2A member. H2A1 and H2AX 
both have an SQ motif, but only H2AX has a complete SQ(E/D)varphi (where varphi 
denotes a hydrophobic residue) known to be phosphorylated in response to DNA 
damage. We show that a novel H2B variant interacts with H2AZ and H2A1 but not 
with H2AX. Chromatin immunoprecipitation (ChIP) revealed that H2AZ and H2Bv are 
enriched at active genes while H2AX is enriched at repressed genes as well as 
the silent TgIRE repeat element. During DNA damage, we detected an increase in 
H2AX phosphorylation as well as increases in h2a1 and h2ax transcription. We 
found that expression of h2ax, but not h2a1 or h2az, increases in bradyzoites 
generated in vitro. Similar analysis performed on mature bradyzoites generated 
in vivo, which are arrested in G0, showed that h2az and h2ax are expressed but 
h2a1 is not, consistent with the idea that h2a1 is the canonical histone 
orthologue in the parasite. The increase of H2AX, which localizes to silenced 
areas during bradyzoite differentiation, is consistent with the quiescent nature 
of this stage of the life cycle. Our results indicate that the early-branching 
eukaryotic parasite Toxoplasma contains nucleosomes of novel composition, which 
is likely to impact multiple facets of parasite biology, including the 
clinically important process of bradyzoite differentiation.