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PMID: 17244705 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 104 ·No. 5 ·2007-01-30 ·Pages 1522-7

Juneau K, Palm C, Miranda M, Davis RW

Abstract

Knowing gene structure is vital to understanding gene function, and accurate genome annotation is essential for understanding cellular function. To this end, we have developed a genome-wide assay for mapping introns in Saccharomyces cerevisiae. Using high-density tiling arrays, we compared wild-type yeast to a mutant deficient for intron degradation. Our method identified 76% of the known introns, confirmed 18 previously predicted introns, and revealed 9 formerly undiscovered introns. Furthermore, we discovered that all 13 meiosis-specific intronic yeast genes undergo regulated splicing, which provides posttranscriptional regulation of the genes involved in yeast cell differentiation. Moreover, we found that approximately 16% of intronic genes in yeast are incompletely spliced during exponential growth in rich medium, which suggests that meiosis is not the only biological process regulated by splicing. Our tiling-array assay provides a snapshot of the spliced transcriptome in yeast. This robust methodology can be used to explore environmentally distinct splicing responses and should be readily adaptable to the study of other organisms, including humans.

MeSH Terms
Alternative Splicing Cell Differentiation Computational Biology Culture Media/metabolism Gene Expression Regulation, Fungal Genes, Fungal Genome, Fungal Introns Meiosis Molecular Sequence Data Oligonucleotide Array Sequence Analysis Open Reading Frames RNA Splicing Saccharomyces cerevisiae/genetics Saccharomyces cerevisiae Proteins/genetics,physiology Software
Chemicals
Culture Media Saccharomyces cerevisiae Proteins
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Juneau Kara
Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA. [email protected]
Palm Curtis
Miranda Molly
Davis Ronald W
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.0610354104
Email
[email protected]
Published
2007-01-30
Epub
2007-00-23
Pages
1522-7
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC1780280
Subset
IM
Grants
NCRR NIH HHS · R21 RR020000 · United States
NCRR NIH HHS · RR020000 · United States
Databases
GENBANK
EF123123, EF123124, EF123125, EF123126, EF123127, EF123128, EF123129, EF123130, EF123131, EF123132, EF123133, EF123134, EF123135, EF123136, EF123137, EF123138, EF123139, EF123140, EF123141, EF123142, EF123143, EF123144, EF123145, EF123146, EF123147, EF123148, EF123149
External Links
PubMed source DOI: 10.1073/pnas.0610354104 PMC Full Text View journal details
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