The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

by: Ugrappa Nagalakshmi, Zhong Wang, Karl Waern, Chong Shou, Debasish Raha, Mark Gerstein, Michael Snyder

Science (1 May 2008), 1158441.

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Abstract

The identification of untranslated regions (UTRs), introns, and coding regions within an organism remains challenging. We developed a quantitative sequencing-based method for mapping transcribed regions called RNA-Seq in which cDNA 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 were also 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. 10.1126/science.1158441

@article{citeulike:2743597, abstract = {The identification of untranslated regions (UTRs), introns, and coding regions within an organism remains challenging. We developed a quantitative sequencing-based method for mapping transcribed regions called RNA-Seq in which cDNA 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 were also 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. 10.1126/science.1158441}, author = {Nagalakshmi, Ugrappa and Wang, Zhong and Waern, Karl and Shou, Chong and Raha, Debasish and Gerstein, Mark and Snyder, Michael }, citeulike-article-id = {2743597}, doi = {http://dx.doi.org/10.1126/science.1158441}, journal = {Science}, keywords = {expression, sequencing, yeast}, month = {May}, pages = {1158441+}, posted-at = {2008-06-10 22:31:03}, priority = {2}, title = {The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing}, url = {http://dx.doi.org/10.1126/science.1158441}, year = {2008} }

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TY - JOUR ID - citeulike:2743597 L3 - citeulike-article-id:2743597 TI - The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing JF - Science SP - 1158441 N2 - The identification of untranslated regions (UTRs), introns, and coding regions within an organism remains challenging. We developed a quantitative sequencing-based method for mapping transcribed regions called RNA-Seq in which cDNA 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 were also 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. 10.1126/science.1158441 KW - expression KW - sequencing KW - yeast AU - Nagalakshmi, Ugrappa AU - Wang, Zhong AU - Waern, Karl AU - Shou, Chong AU - Raha, Debasish AU - Gerstein, Mark AU - Snyder, Michael PY - 2008/05/01/ UR - http://dx.doi.org/10.1126/science.1158441 ER -

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