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dc.contributor.authorChappell, Lia
dc.contributor.authorRoss, Philipp
dc.contributor.authorOrchard, Lindsey
dc.contributor.authorRussell, Timothy J.
dc.contributor.authorOtto, Thomas D.
dc.contributor.authorBerriman, Matthew
dc.contributor.authorRayner, Julian C.
dc.contributor.authorLlinás, Manuel
dc.date.accessioned2021-06-08T15:25:01Z
dc.date.available2021-06-08T15:25:01Z
dc.date.issued2020-06-08
dc.date.submitted2019-12-09
dc.identifier.others12864-020-06787-5
dc.identifier.other6787
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/323590
dc.description.abstractAbstract: 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.
dc.languageen
dc.publisherBioMed Central
dc.subjectResearch Article
dc.subjectEukaryote microbial genomics
dc.titleRefining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq
dc.typeArticle
dc.date.updated2021-06-08T15:24:59Z
prism.issueIdentifier1
prism.publicationNameBMC Genomics
prism.volume21
dc.identifier.doi10.17863/CAM.71049
dcterms.dateAccepted2020-05-19
rioxxterms.versionofrecord10.1186/s12864-020-06787-5
rioxxterms.versionVoR
rioxxterms.licenseref.urihttp://creativecommons.org/licenses/by/4.0/
dc.contributor.orcidLlinás, Manuel [0000-0002-6173-5882]
dc.identifier.eissn1471-2164
pubs.funder-project-idBurroughs Wellcome Fund (1007041.02)
pubs.funder-project-idNational Institutes of Health (1DP2OD001315)
pubs.funder-project-idCenter for Quantitative Biology (P50 GM071508)
pubs.funder-project-idWellcome Trust (206194, 206194, 206194)
pubs.funder-project-idWellcome Trust (206194)


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