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PMID: 15905473 Published · epublish English Journal Article Research Support, Non-U.S. Gov't Validation Study

Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE.

Nucleic acids research ·Vol. 33 ·No. 9 ·2005-00-00 ·Pages 2838-51

Zhang Z, Dietrich FS

Abstract

A minimally addressed area in Saccharomyces cerevisiae research is the mapping of transcription start sites (TSS). Mapping of TSS in S.cerevisiae has the potential to contribute to our understanding of gene regulation, transcription, mRNA stability and aspects of RNA biology. Here, we use 5' SAGE to map 5' TSS in S.cerevisiae. Tags identifying the first 15-17 bases of the transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library. Each clone sequenced from this library identifies 10-20 TSS. We have identified 13,746 unique, unambiguous sequence tags from 2231 S.cerevisiae genes. TSS identified in this study are consistent with published results, with primer extension results described here, and are consistent with expectations based on previous work on transcription initiation. We have aligned the sequence flanking 4637 TSS to identify the consensus sequence A(A(rich))5NPyA(A/T)NN(A(rich))6, which confirms and expands the previous reported PyA(A/T)Pu consensus pattern. The TSS data allowed the identification of a previously unrecognized gene, uncovered errors in previous annotation, and identified potential regulatory RNAs and upstream open reading frames in 5'-untranslated region.

MeSH Terms
Base Sequence Consensus Sequence Gene Expression Profiling/methods Genes, Fungal Genome, Fungal Open Reading Frames Saccharomyces cerevisiae/genetics,metabolism Sequence Tagged Sites Transcription Initiation Site
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Zhang Zhihong
Department of Molecular Genetics and Microbiology, Duke University Medical Center Durham, NC 27710, USA.
Dietrich Fred S
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gki583
Published
2005-00-00
Epub
2005-00-19
Pages
2838-51
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1131933
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gki583 PMC Full Text View journal details
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