Toxoplasma gondii chromatin remodeler SWI/SNF controls parasite division and stage specific gene expression

The SWI/SNF complex is evolutionarily conserved across species, initially identified in yeast, and later associated with various human cancers. In research on Toxoplasma gondii, this complex specifically creates nucleosome-free regions (NFRs) at the promoters of male gamete-specific genes, thereby activating their expression. Disruption of this complex results in the loss of male gametes. Although the SWI/SNF complex is relatively conserved across species, its specific role in T. gondii remains unclear. In this study, we first catalogued the core ATPase subunits of chromatin remodeling complexes and characterized the function of the SWI/SNF ATPase subunits TgSNF2a and TgSNF2b. We found that deletion of these two subunits severely impaired tachyzoite growth and altered the mode of division from endodyogeny to endopolygeny. Disruption of the complex led to a reduction in chromatin accessibility, suppressed stage-specific gene expression during the tachyzoite stage, and indirectly upregulated early endodyogeny stage (EES) genes by downregulating transcriptional repressors such as AP2XII-2 and AP2XII-5, and disrupting interactions with the MORC complex. Consequently, the knockout strains exhibited a shift in gene transcription toward the EES stage. These results provide new insights into the epigenetic regulation of sexual reproduction in T. gondii, offering potential strategies for controlling toxoplasmosis. Overall design: To assess the functions of TgSNF2a and TgSNF2b in T. gondii, an indole-3-acetic acid (IAA) degradation (mAID) system was used to generate inducible knockdown (iKD) of TgSNF2a and TgSNF2b parasites. Double knockdown parasites were also pruduced by using mAID system. Potentially regulated genes of TgSNF2a and TgSNF2b were investigated by RNA-seq using iKD parasites with or without IAA treatment for 24 or 72 hours. Two or three biological replicates were employed. To further characterize the genome occupancy of TgSNF2a and TgSNF2b, CUT&Tag experiments were performed using the endogenously 3xHA tagged parasite and ME49 strain.