Chromatin accessibility based characterization of gene regulatory network of P. falciparum blood stage development. Chromatin accessibility based characterization of gene regulatory network of P. falciparum blood stage development

We present ATAC-seq combined with direction RNA seq data for eight time points across the intraerythorcytic development cycle of Plasmodium falciparum 3D7. ATAC peaks were called by MACS2 using ATAC-seq libraries generated with genomic DNA as a control. The majority of identified ATAC peaks were located in intergenic regions and captured most (95%) of previously identified binding sites of the transcription factor required for the expression of most invasion-related genes PfAP2-I (Santos et al., 2017). The robustness of the ATAC-seq dataset was confirmed with a second biological replicate both in terms of peak location and relative peak accessibility pattern. Peaks were assigned to the closest gene and the majority of peaks showed a clear positive correlation between chromatin accessibility pattern and relative mRNA abundance (Pearson correlation > 0.6). In addition, they were sufficient to drive the stage-specific expression of a reporter gene, demonstrating their functionality. Motif searches restricted to accessible regions showed enrichment of several predicted Plasmodium motifs while also predicting several novel regulatory elements. Overall design: ATAC-seq and RNA-seq at 8 time points across the intraerytrocytic development cycle of P. falciparum 3D7 .