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 journalArticlepeer-review

12 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
Externally publishedYes

Keywords

  • Toxoplasma
  • core promoter
  • transcriptome
  • tss-seq

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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