High-resolution characterization of Toxoplasma gondii transcriptome with a massive parallel sequencing method.
High-resolution characterization of Toxoplasma gondii transcriptome with a massive parallel sequencing method.
复制标题
DOI：
10.1093/dnares/dsq013
复制
发表时间：
2010-08
期刊：
影响因子：
--
通讯作者：
Xuan X
中科院分区：
文献类型：
--
作者：
Yamagishi J;Wakaguri H;Ueno A;Goo YK;Tolba M;Igarashi M;Nishikawa Y;Sugimoto C;Sugano S;Suzuki Y;Watanabe J;Xuan X
在过去的几年中，建立了一种方法，可以收集转录起始位点（tss）的精确位置信息以及高通量的基因表达水平的数字信息。我们应用这种新方法“tss-seq”对刚地弓形虫速殖子的转录组进行了分析，结果鉴定出12.4万个tss，并通过统计分析将它们聚集在1万个转录区（TRs）中。将TRs和带注释的orf配对，结果鉴定出30%的TRs和40%的orf没有对应的TRs，分别预测了未发现的基因和阶段特异性转录。大量的tss数据使得首次对弓形虫核心启动子结构进行系统分析成为可能，这些信息表明，弓形虫利用一个类似于启动子的基序进行转录，该基序位于主要的新基序——下游胸腺嘧啶簇中，与植物中观察到的Y位点相似。这种百科全书式的分析也表明，TATA盒和其他众所周知的核心启动子元素几乎没有被利用。
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.
登录
查看更多内容
影响因子：
4.4
作者：
Callebaut, I;Prat, K;Meurice, E;Mornon, JP;Tomavo, S
通讯作者：
Tomavo, S
影响因子：
4.8
作者：
Brecht, S;Carruthers, VB;Soldati, D
通讯作者：
Soldati, D
影响因子：
14.9
作者：
Balaji S;Babu MM;Iyer LM;Aravind L
通讯作者：
Aravind L
影响因子：
14.9
作者：
Kibe, MK;Coppin, A;Tomavo, S
通讯作者：
Tomavo, S
影响因子：
3
作者：
Jin VX;Singer GA;Agosto-Pérez FJ;Liyanarachchi S;Davuluri RV
通讯作者：
Davuluri RV