High-resolution characterization of toxoplasma gondii transcriptome with a massive parallel sequencing method

Junya Yamagishi, Hiroyuki Wakaguri, Akio Ueno, Youn Kyoung Goo, Mohammed Tolba, Makoto Igarashi, Yoshifumi Nishikawa, Chihiro Sugimoto, Sumio Sugano, Yutaka Suzuki, Junichi Watanabe, Xuenan Xuan

    Research output: Contribution to journalArticle

    8 Citations (Scopus)

    Abstract

    For the last couple of years, a method that permits the collection of precise positional information of transcriptional start sites (TSSs) together with digital information of the gene-expression levels in a high-throughput manner was established. We applied this novel method, 'tss-seq', to elucidate the transcriptome of tachyzoites of the Toxoplasma gondii, which resulted in the identification of 124 000 TSSs, and they were clustered into 10 000 transcription regions (TRs) with a statistics-based analysis. The TRs and annotated ORFs were paired, resulting in the identification of 30 of the TRs and 40 of the ORFs without their counterparts, which predicted undiscovered genes and stage-specific transcriptions, respectively. The massive data for TSSs make it possible to execute the first systematic analysis of the T. gondii core promoter structure, and the information showed that T. gondii utilized an initiator-like motif for their transcription in the major and novel motif, the downstream thymidine cluster, which was similar to the Y patch observed in plants. This encyclopaedic analysis also suggested that the TATA box, and the other well-known core promoter elements were hardly utilized.

    Original languageEnglish
    Pages (from-to)233-243
    Number of pages11
    JournalDNA Research
    Volume17
    Issue number4
    DOIs
    Publication statusPublished - 2010 Aug

    Keywords

    • Toxoplasma
    • core promoter
    • transcriptome
    • tss-seq

    ASJC Scopus subject areas

    • Molecular Biology
    • Genetics

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  • Cite this

    Yamagishi, J., Wakaguri, H., Ueno, A., Goo, Y. K., Tolba, M., Igarashi, M., Nishikawa, Y., Sugimoto, C., Sugano, S., Suzuki, Y., Watanabe, J., & Xuan, X. (2010). High-resolution characterization of toxoplasma gondii transcriptome with a massive parallel sequencing method. DNA Research, 17(4), 233-243. https://doi.org/10.1093/dnares/dsq013