PbAP2-TR plays a role in regulating major transcriptomic changes from early to late trophozoite [PbAP2-TR_ChIP-seq]

To investigate the genome-wide binding sites of PbAP2-TR and PbMORC in the asexual blood stage of Plasmodium berghei, the chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) analyses were performed. Parasites expressing GFP-fused PbAP2-TR or GFP-fused PbMORC were generated from the Cas9-expressing parasite (PbCas9), and pbap2-g was disrupted in these parasites (PbAP2-TR::GFPpbap2-g(-) and PbMORC::GFPpbap2-g(-)). Whole blood was harvested from mice infected with these transgenic parasites at 12 h post infection,and the parasites were then subjected to ChIP-seq experiments using anti-GFP antibody. Genome-wide binding sites of PbAP2-TR were determined from the sequence data. Overall design: PbAP2-TR::GFPpbap2-g(-) and PbMORC::GFPpbap2-g(-) parasites were each cultured for 16 h, and schizonts formed in the cultures were injected into mice. Chromatins associated with GFP-fused PbAP2-TR or PbMORC were IPed with anti-GFP antibody, and DNA fragments purified from the IPed chromoatins were sequenced by the Next Generation Sequencing. Using non-IPed samples as a control (INPUT), binding sites of PbAP2-TR were determined from the sequence data.