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Published online on March 28, 2006, 10.1073/pnas.0601091103
PNAS | April 4, 2006 | vol. 103 | no. 14 | 5320-5325
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BIOLOGICAL SCIENCES / BIOCHEMISTRY
A high-resolution map of transcription in the yeast genome

Lior David*,{dagger}, Wolfgang Huber{dagger},{ddagger}, Marina Granovskaia§, Joern Toedling{ddagger}, Curtis J. Palm*, Lee Bofkin{ddagger}, Ted Jones*, Ronald W. Davis*,¶, and Lars M. Steinmetz*,§,¶

*Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304; {ddagger}European Bioinformatics Institute, European Molecular Biology Laboratory, Cambridge CB10 1SD, United Kingdom; and §European Molecular Biology Laboratory, 69117 Heidelberg, Germany

Contributed by Ronald W. Davis, February 10, 2006

There is abundant transcription from eukaryotic genomes unaccounted for by protein coding genes. A high-resolution genome-wide survey of transcription in a well annotated genome will help relate transcriptional complexity to function. By quantifying RNA expression on both strands of the complete genome of Saccharomyces cerevisiae using a high-density oligonucleotide tiling array, this study identifies the boundary, structure, and level of coding and noncoding transcripts. A total of 85% of the genome is expressed in rich media. Apart from expected transcripts, we found operon-like transcripts, transcripts from neighboring genes not separated by intergenic regions, and genes with complex transcriptional architecture where different parts of the same gene are expressed at different levels. We mapped the positions of 3' and 5' UTRs of coding genes and identified hundreds of RNA transcripts distinct from annotated genes. These nonannotated transcripts, on average, have lower sequence conservation and lower rates of deletion phenotype than protein coding genes. Many other transcripts overlap known genes in antisense orientation, and for these pairs global correlations were discovered: UTR lengths correlated with gene function, localization, and requirements for regulation; antisense transcripts overlapped 3’ UTRs more than 5’ UTRs; UTRs with overlapping antisense tended to be longer; and the presence of antisense associated with gene function. These findings may suggest a regulatory role of antisense transcription in S. cerevisiae. Moreover, the data show that even this well studied genome has transcriptional complexity far beyond current annotation.

tiling array | transcriptone survey | gene architecture | segmentation | antisense regulation

Freely available online through the PNAS open access option.

{dagger}L.D. and W.H. contributed equally to this work.

Author contributions: W.H., R.W.D., and L.M.S. designed research; L.D., W.H., M.G., and L.M.S. performed research; C.J.P. and T.J. contributed new reagents/analytic tools; L.D., W.H., M.G., J.T., L.B., and L.M.S. analyzed data; and L.D., W.H., and L.M.S. wrote the paper.

Conflict of interest statement: No conflicts declared.

Data deposition: The array data have been deposited in ArrayExpress database (accession no. E-TABM-14).

To whom correspondence may be addressed. E-mail: dbowe{at}stanford.edu or larsms{at}embl.de

© 2006 by The National Academy of Sciences of the USA


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