Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq

Chappell, L., Ross, P., Orchard, L., Russell, T. J., Otto, T. D. , Berriman, M., Rayner, J. C. and Llinás, M. (2020) Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq. BMC Genomics, 21, 395. (doi: 10.1186/s12864-020-06787-5)

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Abstract

Background: Plasmodium parasites undergo several major developmental transitions during their complex lifecycle, which are enabled by precisely ordered gene expression programs. Transcriptomes from the 48-h blood stages of the major human malaria parasite Plasmodium falciparum have been described using cDNA microarrays and RNA-seq, but these assays have not always performed well within non-coding regions, where the AT-content is often 90–95%. Results: We developed a directional, amplification-free RNA-seq protocol (DAFT-seq) to reduce bias against AT-rich cDNA, which we have applied to three strains of P. falciparum (3D7, HB3 and IT). While strain-specific differences were detected, overall there is strong conservation between the transcriptional profiles. For the 3D7 reference strain, transcription was detected from 89% of the genome, with over 78% of the genome transcribed into mRNAs. We also find that transcription from bidirectional promoters frequently results in non-coding, antisense transcripts. These datasets allowed us to refine the 5′ and 3′ untranslated regions (UTRs), which can be variable, long (> 1000 nt), and often overlap those of adjacent transcripts. Conclusions: The approaches applied in this study allow a refined description of the transcriptional landscape of P. falciparum and demonstrate that very little of the densely packed P. falciparum genome is inactive or redundant. By capturing the 5′ and 3′ ends of mRNAs, we reveal both constant and dynamic use of transcriptional start sites across the intraerythrocytic developmental cycle that will be useful in guiding the definition of regulatory regions for use in future experimental gene expression studies.

Item Type:Articles
Additional Information:M.L. received support from the Burroughs Wellcome Fund for Investigators in Pathogenesis of Infectious Disease (1007041.02), National Institutes of Health Grant (1DP2OD001315), and Center for Quantitative Biology Grant (P50 GM071508). L.C., T.D.O., M.B. and J.R. were supported by the Wellcome Trust through a core grant to the Wellcome Sanger Institute (206194).
Keywords:Research Article, Eukaryote microbial genomics.
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Otto, Dr Thomas
Authors: Chappell, L., Ross, P., Orchard, L., Russell, T. J., Otto, T. D., Berriman, M., Rayner, J. C., and Llinás, M.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:BMC Genomics
Publisher:BioMed Central
ISSN:1471-2164
ISSN (Online):BMC Genomics
Copyright Holders:Copyright © 2020 The Authors
First Published:First published in BMC Genomics 21:395
Publisher Policy:Reproduced under a Creative Commons licence

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