Abstract
Background. The genome of the human malaria parasite Plasmodium falciparum is poorly annotated, in particular, the 50 capped ends of its mRNA transcripts. New approaches are needed to fully catalog P. falciparum transcripts for understanding gene function and regulation in this organism. Methods.Wedeveloped a transcriptomic method based on next-generation sequencing of complementary DNA (cDNA) enriched for full-length fragments using eIF4E, a 50 cap-binding protein, and an unenriched control. DNA sequencing adapter was added after enrichment of full-length cDNA using two different ligation protocols. From the mapped sequence reads, enrichment scores were calculated for all transcribed nucleotides and used to calculate P-values of 50 capped nucleotide enrichment. Sensitivity and accuracy were increased by combining P-values from replicate experiments. Data were obtained for P. falciparum ring, trophozoite and schizont stages of intraerythrocytic development. Results. 50 capped nucleotide signals were mapped to 17,961 non-overlapping P. falciparum genomic intervals. Analysis of the dominant 50 capped nucleotide in these genomic intervals revealed the presence of two groups with distinctive epigenetic features and sequence patterns. A total of 4,512 transcripts were annotated as 50 capped based on the correspondence of 50 end with 50 capped nucleotide annotated from fulllength cDNA data. Discussion. The presence of two groups of 50 capped nucleotides suggests that alternative mechanisms may exist for producing 50 capped transcript ends in P. falciparum. The 50 capped transcripts that are antisense, outside of, or partially overlapping coding regions may be important regulators of gene function in P. falciparum. ©Copyright 2021 Shaw et al.
