A large-scale full-length cDNA analysis to explore the budding yeast transcriptome
A large-scale full-length cDNA analysis to explore the budding yeast transcriptome
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DOI：
10.1073/pnas.0605645103
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发表时间：
2006-11-21
影响因子：
11.1
通讯作者：
Ito, Takashi
中科院分区：
文献类型：
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作者：
Miura, Fumihito;Kawaguchi, Noriko;Ito, Takashi
我们进行了大规模 cDNA 分析，以探索芽殖酵母酿酒酵母的转录组。我们对两个 cDNA 文库进行了测序，一个来自在基本培养基中指数生长的细胞，另一个来自减数分裂细胞。这两个文库都是使用矢量加帽方法生成的，该方法可以准确定位转录起始位点 (TSS)。因此，我们鉴定了 11,575 个 TSS，与 3,638 个带注释的基因组特征相关，包括 3,599 个 ORF，表明大多数酵母基因具有两个或多个 TSS。此外，我们还鉴定了 45 个先前未描述的内含子，包括影响当前 ORF 注释的内含子和交替剪接的内含子。此外，分析揭示了基因间区域中的 667 个转录单位和源自 367 个已知特征的反义链的转录本。我们还发现 348 个 ORF 在其 3' 半部分携带 TSS，以从 ORF 内部开始生成有义转录本。这些结果表明，芽殖酵母转录组比以前认为的要复杂得多，并且它与哺乳动物和其他高等真核生物的转录组具有许多最近揭示的特征。因此，产生新型转录物的全基因组活性转录似乎是真核细胞的固有特征。芽殖酵母将作为转录组这些方面研究的通用模型，而全长 cDNA 克隆可以作为此类研究的宝贵资源。
We performed a large-scale cDNA analysis to explore the transcriptome of the budding yeast Saccharomyces cerevisiae. We sequenced two cDNA libraries, one from the cells exponentially growing in a minimal medium and the other from meiotic cells. Both libraries were generated by using a vector-capping method that allows the accurate mapping of transcription start sites (TSSs). Consequently, we identified 11,575 TSSs associated with 3,638 annotated genomic features, including 3,599 ORFs, to suggest that most yeast genes have two or more TSSs. In addition, we identified 45 previously undescribed introns, including those affecting current ORF annotations and those spliced alternatively. Furthermore, the analysis revealed 667 transcription units in the intergenic regions and transcripts derived from antisense strands of 367 known features. We also found that 348 ORFs carry TSSs in their 3'-halves to generate sense transcripts starting from inside the ORFs. These results indicate that the budding yeast transcriptome is considerably more complex than previously thought, and it shares many recently revealed characteristics with the transcriptomes of mammals and other higher eukaryotes. Thus, the genome-wide active transcription that generates novel classes of transcripts appears to be an intrinsic feature of the eukaryotic cells. The budding yeast will serve as a versatile model for the studies on these aspects of transcriptome, and the full-length cDNA clones can function as an invaluable resource in such studies.