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

BMC Genomics

Pardis C Sabeti⁴  John L Rinn¹  Dyann Wirth⁵  Ulf Ribacke³  Jill C Broadbent⁴  Kate M Broadbent² 

[1] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA;Broad Institute, Cambridge, Massachusetts, USA;Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden;Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA;Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA

关键词: PfGDV1;    Extreme genome;    Gene regulation;    Transcriptome;    Plasmodium;    Malaria;    microRNA;    circRNA;    Antisense RNA;    lncRNA;    Non-coding RNA;    RNA sequencing;   

Others  :  1213741
DOI  :  10.1186/s12864-015-1603-4

实施日期：2015-05-01，发布日期：2015-06-13

【 摘 要 】

Background

The 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.

Results

To 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.

Conclusions

We 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.

【 授权许可】

   
2015 Broadbent et al.

【 图 表 】

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