The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome
The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome
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DOI：
10.1073/pnas.201182798
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发表时间：
2001-10-09
影响因子：
11.1
通讯作者：
de Souza, SJ
中科院分区：
文献类型：
--
作者：
Camargo, AA;Samaia, HPB;de Souza, SJ
开放阅读框表达序列标签（ORESTES）与常规EST的不同之处在于提供来自转录物的中心蛋白质编码部分的序列数据。我们从24种人体组织中总共生成了696，745个ORESTES序列，并使用了对应于一组15，095个全长mRNA的数据子集作为评估策略效率及其对人类转录组定义的潜在贡献的手段。我们估计，ORESTES对所有高度和中度表达的人类基因中的80%以上以及40%至50%的罕见表达的人类基因进行了采样。在我们最彻底测序的组织--乳腺中，产生的130，000个ORESTES来自该组织中表达的所有基因的约70%的转录本，高表达和低表达基因的表达效率相同。在这方面，我们发现，能力的ORESTES战略的基因发现和鸟枪转录序列生成显着超过传统的EST。ORESTES的分布使得许多人类转录物现在由沿着每个基因产物的长度分布的部分序列的支架表示。实验连接的支架组件，通过逆转录-PCR，代表一个直接的路线，转录整理，可能代表一个有用的替代全长cDNA克隆。
open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data from the central protein coding portion of transcripts. We generated a total of 696,745 ORESTES sequences from 24 human tissues and used a subset of the data that correspond to a set of 15,095 full-length mRNAs as a means of assessing the efficiency of the strategy and its potential contribution to the definition of the human transcriptome. We estimate that ORESTES sampled over 80% of all highly and moderately expressed, and between 40% and 50% of rarely expressed, human genes. In our most thoroughly sequenced tissue, the breast, the 130,000 ORESTES generated are derived from transcripts from an estimated 70% of all genes expressed in that tissue, with an equally efficient representation of both highly and poorly expressed genes. In this respect, we find that the capacity of the ORESTES strategy both for gene discovery and shotgun transcript sequence generation significantly exceeds that of conventional ESTs. The distribution of ORESTES is such that many human transcripts are now represented by a scaffold of partial sequences distributed along the length of each gene product. The experimental joining of the scaffold components, by reverse transcription-PCR, represents a direct route to transcript finishing that may represent a useful alternative to full-length cDNA cloning.