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

被引:146
作者
Broadbent, Kate M. [1 ,2 ]
Broadbent, Jill C. [3 ,4 ]
Ribacke, Ulf [5 ,6 ]
Wirth, Dyann [2 ,5 ]
Rinn, John L. [1 ,2 ,7 ]
Sabeti, Pardis C. [1 ,2 ,3 ,4 ]
机构
[1] Harvard Univ, Sch Med, Dept Syst Biol, Boston, MA 02115 USA
[2] Broad Inst, Cambridge, MA USA
[3] Harvard Univ, FAS Ctr Syst Biol, Boston, MA 02115 USA
[4] Harvard Univ, Dept Organism & Evolutionary Biol, Boston, MA 02115 USA
[5] Harvard Univ, Sch Publ Hlth, Dept Immunol & Infect Dis, Boston, MA 02115 USA
[6] Uppsala Univ, BMC, Dept Cell & Mol Biol, Uppsala, Sweden
[7] Harvard Univ, Dept Stem Cell & Regenerat Biol, Boston, MA 02115 USA
来源
BMC GENOMICS | 2015年 / 16卷
关键词
RNA sequencing; Non-coding RNA; lncRNA; Antisense RNA; circRNA; microRNA; Malaria; Plasmodium; Transcriptome; Gene regulation; Extreme genome; PfGDV1; NATURAL ANTISENSE TRANSCRIPTS; GENE-EXPRESSION; EPIGENETIC REGULATION; ANTIGENIC VARIATION; COMPARATIVE GENOMICS; SEXUAL DEVELOPMENT; PCR AMPLIFICATION; SPLICE JUNCTIONS; QUALITY-CONTROL; PARASITE;
D O I
10.1186/s12864-015-1603-4
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
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.
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页数:22
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