Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNAReportar como inadecuado

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BMC Genomics

, 16:454

First Online: 13 June 2015Accepted: 01 May 2015DOI: 10.1186-s12864-015-1603-4

Cite this article as: Broadbent, K.M., Broadbent, J.C., Ribacke, U. et al. BMC Genomics 2015 16: 454. doi:10.1186-s12864-015-1603-4


BackgroundThe human malaria parasite Plasmodium falciparum has a complex and multi-stage life cycle that requires extensive and precise gene regulation to allow invasion and hijacking of host cells, transmission, and immune escape. To date, the regulatory elements orchestrating these critical parasite processes remain largely unknown. Yet it is becoming increasingly clear that long non-coding RNAs lncRNAs could represent a missing regulatory layer across a broad range of organisms.

ResultsTo investigate the regulatory capacity of lncRNA in P. falciparum, we harvested fifteen samples from two time-courses. Our sample set profiled 56 h of P. falciparum blood stage development. We then developed and validated strand-specific, non-polyA-selected RNA sequencing methods, and pursued the first assembly of P. falciparum strand-specific transcript structures from RNA sequencing data. This approach enabled the annotation of over one thousand lncRNA transcript models and their comprehensive global analysis: coding prediction, periodicity, stage-specificity, correlation, GC content, length, location relative to annotated transcripts, and splicing. We validated the complete splicing structure of three lncRNAs with compelling properties. Non-polyA-selected deep sequencing also enabled the prediction of hundreds of intriguing P. falciparum circular RNAs, six of which we validated experimentally.

ConclusionsWe found that a subset of lncRNAs, including all subtelomeric lncRNAs, strongly peaked in expression during invasion. By contrast, antisense transcript levels significantly dropped during invasion. As compared to neighboring mRNAs, the expression of antisense-sense pairs was significantly anti-correlated during blood stage development, indicating transcriptional interference. We also validated that P. falciparum produces circRNAs, which is notable given the lack of RNA interference in the organism, and discovered that a highly expressed, five-exon antisense RNA is poised to regulate P. falciparum gametocyte development 1 PfGDV1, a gene required for early sexual commitment events.

KeywordsRNA sequencing Non-coding RNA lncRNA Antisense RNA circRNA microRNA Malaria Plasmodium Transcriptome Gene regulation Extreme genome PfGDV1 AbbreviationslncRNAsLong non-coding RNAs

RBCRed blood cell

CVGEClonally variant gene expression

PfEMP1P. falciparum Erythrocyte Membrane Protein 1

CLAG3Cytoadherence Linked Asexual Gene 3

RISCRNA-induced silencing complex

circRNAcircular RNA

hpihours post-infection


CVCoefficient of variation

MDSMultidimenstional scaling

mRNAmessenger RNA

RABTReference-annotation based transcript assembly

FPKMFragments per kilobase of exon per million fragments mapped

UTRUntranslated region

ETRAMPEarly Transcribed Membrane Protein

PfGDV1P. falciparum Gametocyte Development Protein 1

ARPApoptosis-related protein

cDNAcomplementary DNA

gDNAgenomic DNA

MCA2Metacaspase-like protein

PNAPeptide nucleic acid

FSSFirst strand synthesis

SSSSecond strand synthesis

USERUracil-Specific Excision Reagent

PFPassing Illumina filtering


TARETelomere-associated repetitive element

John L Rinn and Pardis C Sabeti contributed equally to this work.

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-015-1603-4 contains supplementary material, which is available to authorized users.

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Autor: Kate M Broadbent - Jill C Broadbent - Ulf Ribacke - Dyann Wirth - John L Rinn - Pardis C Sabeti


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