{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,19]],"date-time":"2025-08-19T10:53:32Z","timestamp":1755600812745},"reference-count":87,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2021,8,25]],"date-time":"2021-08-25T00:00:00Z","timestamp":1629849600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The Platform Technology Management section, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand.","award":["P1201270","P1551103"],"award-info":[{"award-number":["P1201270","P1551103"]}]},{"DOI":"10.13039\/501100004396","name":"The Thailand Research Fund","doi-asserted-by":"crossref","award":["RSA5880064"],"award-info":[{"award-number":["RSA5880064"]}],"id":[{"id":"10.13039\/501100004396","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004192","name":"The National Science and Technology Development Agency,","doi-asserted-by":"crossref","award":["P1300832","P1850116","P1450883"],"award-info":[{"award-number":["P1300832","P1850116","P1450883"]}],"id":[{"id":"10.13039\/501100004192","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:sec>\n               <jats:title>Background<\/jats:title>\n               <jats:p>The genome of the human malaria parasite <jats:italic>Plasmodium falciparum<\/jats:italic> is poorly annotated, in particular, the 5\u2032\u00a0capped ends of its mRNA transcripts. New approaches are needed to fully catalog <jats:italic>P. falciparum<\/jats:italic> transcripts for understanding gene function and regulation in this organism.<\/jats:p>\n            <\/jats:sec>\n            <jats:sec>\n               <jats:title>Methods<\/jats:title>\n               <jats:p>We developed a transcriptomic method based on next-generation sequencing of complementary DNA (cDNA) enriched for full-length fragments using eIF4E, a 5\u2032\u00a0cap-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 <jats:italic>P<\/jats:italic>-values of 5\u2032\u00a0capped nucleotide enrichment. Sensitivity and accuracy were increased by combining <jats:italic>P<\/jats:italic>-values from replicate experiments. Data were obtained for <jats:italic>P. falciparum<\/jats:italic> ring, trophozoite and schizont stages of intra-erythrocytic development.<\/jats:p>\n            <\/jats:sec>\n            <jats:sec>\n               <jats:title>Results<\/jats:title>\n               <jats:p>5\u2032\u00a0capped nucleotide signals were mapped to 17,961 non-overlapping <jats:italic>P. falciparum<\/jats:italic> genomic intervals. Analysis of the dominant 5\u2032\u00a0capped 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 5\u2032\u00a0capped based on the correspondence of 5\u2032\u00a0end with 5\u2032\u00a0capped nucleotide annotated from full-length cDNA data.<\/jats:p>\n            <\/jats:sec>\n            <jats:sec>\n               <jats:title>Discussion<\/jats:title>\n               <jats:p>The presence of two groups of 5\u2032\u00a0capped nucleotides suggests that alternative mechanisms may exist for producing 5\u2032\u00a0capped transcript ends in <jats:italic>P. falciparum.<\/jats:italic> The 5\u2032\u00a0capped transcripts that are antisense, outside of, or partially overlapping coding regions may be important regulators of gene function in <jats:italic>P. falciparum<\/jats:italic>.<\/jats:p>\n            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