The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

TLDR

The identification of untranslated regions, introns, and coding regions within an organism remains challenging. We developed RNA‑Seq, a quantitative sequencing‑based method for mapping transcribed regions by sequencing cDNA fragments and aligning them to the genome. We applied RNA‑Seq to generate a high‑resolution transcriptome map of the yeast genome, revealing that 74.5 % of its non‑repetitive sequence is transcribed. The RNA‑Seq analysis confirmed many known and predicted introns, identified alternative initiation codons and upstream open reading frames, revealed unexpected 3′‑end heterogeneity and overlapping genes, and showed that the yeast transcriptome is more complex than previously appreciated.

Abstract

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.