Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum
Top Cited Papers
Open Access
- 30 November 2011
- journal article
- research article
- Published by Springer Science and Business Media LLC in BMC Genomics
- Vol. 12 (1), 1-13
- https://doi.org/10.1186/1471-2164-12-587
Abstract
Background: It has been shown that nearly a quarter of the initial predicted gene models in the Plasmodium falciparum genome contain errors. Although there have been efforts to obtain complete cDNA sequences to correct the errors, the coverage of cDNA sequences on the predicted genes is still incomplete, and many gene models for those expressed in sexual or mosquito stages have not been validated. Antisense transcripts have widely been reported in P. falciparum; however, the extent and pattern of antisense transcripts in different developmental stages remain largely unknown. Results: We have sequenced seven bidirectional libraries from ring, early and late trophozoite, schizont, gametocyte II, gametocyte V, and ookinete, and four strand-specific libraries from late trophozoite, schizont, gametocyte II, and gametocyte V of the 3D7 parasites. Alignment of the cDNA sequences to the 3D7 reference genome revealed stage-specific antisense transcripts and novel intron-exon splicing junctions. Sequencing of strand-specific cDNA libraries suggested that more genes are expressed in one direction in gametocyte than in schizont. Alternatively spliced genes, antisense transcripts, and stage-specific expressed genes were also characterized. Conclusions: It is necessary to continue to sequence cDNA from different developmental stages, particularly those of non-erythrocytic stages. The presence of antisense transcripts in some gametocyte and ookinete genes suggests that these antisense RNA may play an important role in gene expression regulation and parasite development. Future gene expression studies should make use of directional cDNA libraries. Antisense transcripts may partly explain the observed discrepancy between levels of mRNA and protein expression.Keywords
This publication has 47 references indexed in Scilit:
- Effect of PCR extension temperature on high-throughput sequencingMolecular and Biochemical Parasitology, 2011
- NSR-seq transcriptional profiling enables identification of a gene signature of Plasmodium falciparum parasites infecting childrenJCI Insight, 2011
- RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcriptsNucleic Acids Research, 2011
- RNA sequencing: advances, challenges and opportunitiesNature Reviews Genetics, 2010
- H2A.Z Demarcates Intergenic Regions of the Plasmodium falciparum Epigenome That Are Dynamically Marked by H3K9ac and H3K4me3PLoS Pathogens, 2010
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiationNature Biotechnology, 2010
- New insights into the blood‐stage transcriptome of Plasmodium falciparum using RNA‐SeqMolecular Microbiology, 2010
- Universal Features of Post-Transcriptional Gene Regulation Are Critical for Plasmodium Zygote DevelopmentPLoS Pathogens, 2010
- A global view of the nonprotein-coding transcriptome in Plasmodium falciparumNucleic Acids Research, 2009
- Inhibition of Plasmodium falciparum clag9 gene function by antisense RNAMolecular and Biochemical Parasitology, 2000