Justin Gibbons
Swamy R. Adapa
Jenna Oberstaller
Xiangyun Liao
Min Zhang
John H. Adams
Rays H.Y. Jiang
Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
More InformationCorresponding author: E-mail address: Jiang2@usf.edu (Rays H.Y. Jiang)
Publish Date:2020-09-25
Abstract
Abstract
The human malaria parasite Plasmodium falciparum thrives in radically different host environments in mosquitoes and humans, with only a limited set of transcription factors. The nature of regulatory elements or their target genes in the P.?falciparum genome remains elusive. Here, we found that this eukaryotic parasite uses an efficient way to maximally use genetic and epigenetic regulation to form regulatory units (RUs) during blood infections. Genes located in the same RU tend to have the same pattern of expression over time and are associated with open chromatin along regulatory elements. To precisely define and quantify these RUs, a novel hidden Markov model was developed to capture the regulatory structure in a genome-wide fashion by integrating expression and epigenetic evidence. We successfully identified thousands of RUs and cross-validated with previous findings. We found more genes involved in red blood cell (RBC) invasion located in the same RU as the PfAP2-I (AP2-I) transcription factor, demonstrating that AP2-I is responsible for regulating RBC invasion. Our study has provided a regulatory mechanism for a compact eukaryotic genome?and offers new insights into thein?vivo transcriptional regulation of the P.?falciparum intraerythrocytic stage.Keywords: Gene regulation,
Regulatory units,
ATAC-Seq,
RNA-Seq,
Hidden Markov Model,
Malaria
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