An ISWI-related chromatin remodeler orchestrates parasite lifecycle progression by insulating gene expression in a densely packed genome [RNA-seq]
In eukaryotic cells, ATP-dependent chromatin remodelers are specialized multiprotein machines that organize the genome and rule its accessibility by repositioning, ejecting or modifying nucleosomes, but their role in Toxoplasma gondii is still poorly understood. Phylogenetic analyzes show that the parasite retains the four commonly recognized remodeler families and has evolved two divergent proteins within the ISWI family: TgSNF2h and TgSNF2L. These proteins are structurally divergent and form distinct complexes. TgSNF2h specifically forms a core complex with the transcription factor AP2VIII-2 and the scaffold protein TgRFTS. Depletion of TgRFTS phenocopies the knockdown of TgSNF2h, restricting access to chromatin and altering local gene expression. At the genomic level, TgSNF2h actively insulates highly transcribed genes from their minimally expressed or silenced neighbors. This ISWI complex establishes and maintains stage-specific gene expression by regulating the chromatin accessibility to transcription factors. Using MORC as a proxy, we have shown that TgSNF2h rules DNA accessibility and thereby exerts an epistatic control over a key regulator of sexual commitment. In a parasite characterized by high phenotypic plasticity and a compact genome, this dedicated ISWI complex orchestrates the partitioning of developmental genes and ensures transcriptional fidelity throughout its life cycle. Overall design: We report transcriptome of RH Ku80 SNF2h KD and  RH Ku80 RFTS KD in Toxoplasma gondii tachyzoites left untreated or after 24 h of IAA treatment using Nanopore Direct RNA sequencing and Illumina RNA sequencing.