Publication Date:
2008-05-03
Description:
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.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951732/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951732/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nagalakshmi, Ugrappa -- Wang, Zhong -- Waern, Karl -- Shou, Chong -- Raha, Debasish -- Gerstein, Mark -- Snyder, Michael -- P50 HG002357/HG/NHGRI NIH HHS/ -- P50 HG002357-10/HG/NHGRI NIH HHS/ -- R01 CA077808/CA/NCI NIH HHS/ -- R01 CA077808-12/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2008 Jun 6;320(5881):1344-9. doi: 10.1126/science.1158441. Epub 2008 May 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18451266" target="_blank"〉PubMed〈/a〉
Keywords:
Algorithms
;
Codon, Initiator
;
Computational Biology
;
DNA, Complementary
;
DNA, Intergenic
;
*Gene Expression Profiling
;
Genes, Fungal
;
*Genome, Fungal
;
Genomics
;
Introns
;
Open Reading Frames
;
RNA, Fungal/genetics
;
Saccharomyces cerevisiae/*genetics
;
*Sequence Analysis, RNA
;
*Transcription, Genetic
;
Untranslated Regions
Print ISSN:
0036-8075
Electronic ISSN:
1095-9203
Topics:
Biology
,
Chemistry and Pharmacology
,
Computer Science
,
Medicine
,
Natural Sciences in General
,
Physics
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