High-resolution characterization of Toxoplasma gondii transcriptome with a massive parallel sequencing method.
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.
1National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan.
Junya
J
Yamagishi
Hiroyuki
H
Wakaguri
Akio
A
Ueno
Youn-Kyoung
YK
Goo
Mohammed
M
Tolba
Makoto
M
Igarashi
Yoshifumi
Y
Nishikawa
Chihiro
C
Sugimoto
Sumio
S
Sugano
Yutaka
Y
Suzuki
Junichi
J
Watanabe
Xuenan
X
Xuan
D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods*; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*; D016385:TATA Box / Q000235:genetics; D014122:Toxoplasma / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
D014157:Transcription Factors