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

BMC Genomics
Lia ChappellManuel Llinás

Abstract

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%. 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. The approaches applied in this study allow a refined description of the transcrip...Continue Reading

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Citations

Feb 2, 2021·Frontiers in Cellular and Infection Microbiology·Yiran LiJessica C Kissinger
Mar 13, 2021·Frontiers in Cellular and Infection Microbiology·Mengquan YangQingfeng Zhang
Apr 27, 2021·Frontiers in Cellular and Infection Microbiology·Marta MachadoMarkus Ganter
May 8, 2021·RNA Biology·Diana Renteria AlvarezKausik Chakrabarti
Jun 5, 2021·Nature Reviews. Microbiology·Johanna Hoshizaki, Marcus C S Lee
Jun 3, 2021·Genes·Mirko Pegoraro, Gareth D Weedall
Sep 17, 2021·PeerJ·Philip J ShawSissades Tongsima

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Methods Mentioned

BETA
RNA-seq
PCR
Illumina sequencing
DAFT-seq
Smart-seq2
chip

Software Mentioned

CAGEr
Lia
SMALT
TopGO
TopHat2
BEDtools
FIMO
Artemis genome browser
house Perl scripts Chappell
MEME

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