The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
Ugrappa Nagalakshmi,1*
Zhong Wang,1*
Karl Waern,1
Chong Shou,2
Debasish Raha,1
Mark Gerstein,2,3
Michael Snyder1,2,3
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.
1 Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.
2 Program in Computer Science and Computational Biology, Yale University, New Haven, CT 06520, USA.
3 Department of Molecular, Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
* These authors contributed equally to this work.
To whom correspondence should be addressed. E-mail: michael.snyder{at}yale.edu
