通过虚拟Northern RNA测序分析估计恶性疟原虫基因的mRNA长度

Estimating mRNA lengths from Plasmodium falciparum genes by Virtual Northern RNA-seq analysis.

作者信息

Shaw Philip J, Kaewprommal Pavita, Piriyapongsa Jittima, Wongsombat Chayaphat, Yuthavong Yongyuth, Kamchonwongpaisan Sumalee

机构信息

Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Thanon Phahonyothin, Tambon Khlong Neung, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.

Biostatistics and Bioinformatics Laboratory, Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Thanon Phahonyothin, Tambon Khlong Neung, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.

出版信息

Int J Parasitol. 2016 Jan;46(1):7-12. doi: 10.1016/j.ijpara.2015.09.007. Epub 2015 Nov 10.

DOI:10.1016/j.ijpara.2015.09.007

PMID:26548960

Abstract

Accurate gene models are essential for understanding parasite biology. However, transcript structure information is lacking for most parasite genes. Here, we describe "Virtual Northern" analysis of the malaria parasite Plasmodium falciparum to address this issue. RNA-seq libraries were made from size-fractionated RNA. Transcript sizes for 3052 genes were inferred from the read counts in each library. The data show that for almost half of the transcripts, the combined untranslated regions are more than twice the length of the open reading frame. Furthermore, we identified novel polycistronic, or gene overlapping, transcripts that suggest revisions to current gene models are needed.

摘要

准确的基因模型对于理解寄生虫生物学至关重要。然而，大多数寄生虫基因缺乏转录本结构信息。在此，我们描述了对疟原虫恶性疟原虫的“虚拟Northern”分析以解决这一问题。RNA-seq文库由大小分级的RNA构建而成。从每个文库中的读数计数推断出3052个基因的转录本大小。数据表明，对于几乎一半的转录本，组合的非翻译区长度超过开放阅读框长度的两倍。此外，我们鉴定出了新的多顺反子或基因重叠转录本，这表明需要对当前的基因模型进行修订。