Nagalakshmi Ugrappa, Wang Zhong, Waern Karl, Shou Chong, Raha Debasish, Gerstein Mark, Snyder Michael
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.
Science. 2008 Jun 6;320(5881):1344-9. doi: 10.1126/science.1158441. Epub 2008 May 1.
The identification of untranslated regions, introns, and coding regions within an organism remains challenging. We developed a quantitative sequencing-based method called RNA-Seq for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome. We applied RNA-Seq to generate a high-resolution transcriptome map of the yeast genome and demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed. We confirmed many known and predicted introns and demonstrated that others are not actively used. Alternative initiation codons and upstream open reading frames also were identified for many yeast genes. We also found unexpected 3'-end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated.
在一个生物体中识别非翻译区、内含子和编码区仍然具有挑战性。我们开发了一种基于定量测序的方法，称为RNA测序（RNA-Seq），用于绘制转录区域，其中互补DNA片段经过高通量测序并映射到基因组上。我们应用RNA测序生成了酵母基因组的高分辨率转录组图谱，并证明酵母基因组中大多数（74.5%）的非重复序列都被转录。我们证实了许多已知的和预测的内含子，并证明其他一些内含子并未被积极使用。许多酵母基因还鉴定出了替代起始密码子和上游开放阅读框。我们还发现了意外的3'端异质性以及许多重叠基因的存在。这些结果表明酵母转录组比以前认为的更为复杂。
