Abstract
AbstractMalaria remains one of the deadliest infectious diseases. Transcriptional regulation effects of noncoding variants in this unusual genome of malaria parasites remain elusive. We developed a sequence-based,ab initiodeep learning framework, MalariaSED, for predicting chromatin profiles in malaria parasites. The MalariaSED performance was validated by published ChIP-qPCR and TF motifs results. Applying MalariaSED to ~1.3 million variants showed that geographically differentiated noncoding variants are associated with parasite invasion and drug resistance. Further analysis revealed chromatin accessibility changes atP. falciparumrings are partly associated with artemisinin resistance. MalariaSED illuminates the potential functional roles of noncoding variants in malaria parasites.
Publisher
Cold Spring Harbor Laboratory