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Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae.

Hurowitz EH, Brown PO - Genome Biol. (2003)

Bottom Line: We found a close linear relationship between mRNA lengths and the lengths of known or predicted translated sequences; mRNAs were typically around 300 nucleotides longer than the translated sequences.Interestingly, we found that systematic differences in the total length of the untranslated sequences in mRNAs were related to the functions of the encoded proteins.A systematic relationship between the lengths of the untranslated regions in yeast mRNAs and the functions of the proteins they encode may point to an important regulatory role for these sequences.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA.

ABSTRACT

Background: Although the protein-coding sequences in the Saccharomyces cerevisiae genome have been studied and annotated extensively, much less is known about the extent and characteristics of the untranslated regions of yeast mRNAs.

Results: We developed a 'Virtual Northern' method, using DNA microarrays for genome-wide systematic analysis of mRNA lengths. We used this method to measure mRNAs corresponding to 84% of the annotated open reading frames (ORFs) in the S. cerevisiae genome, with high precision and accuracy (measurement errors +/- 6-7%). We found a close linear relationship between mRNA lengths and the lengths of known or predicted translated sequences; mRNAs were typically around 300 nucleotides longer than the translated sequences. Analysis of genes deviating from that relationship identified ORFs with annotation errors, ORFs that appear not to be bona fide genes, and potentially novel genes. Interestingly, we found that systematic differences in the total length of the untranslated sequences in mRNAs were related to the functions of the encoded proteins.

Conclusions: The Virtual Northern method provides a practical and efficient method for genome-scale analysis of transcript lengths. Approximately 12-15% of the yeast genome is represented in untranslated sequences of mRNAs. A systematic relationship between the lengths of the untranslated regions in yeast mRNAs and the functions of the proteins they encode may point to an important regulatory role for these sequences.

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Related in: MedlinePlus

Virtual Northern scheme.
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Figure 1: Virtual Northern scheme.

Mentions: The Virtual Northern scheme is summarized in Figure 1. Poly(A) RNA is separated by length on an agarose gel. The gel is sliced into a large number of thin slices, each of which contains RNAs from a narrow range of lengths [8]. RNA from each slice is then recovered, fluorescently labeled, and hybridized to a separate DNA microarray. Systematic analysis of the variation in the hybridization signal - across the series of gel slices for each DNA sequence represented on the microarrays - gives the length profile of all the transcripts that contain that sequence (Figure 2). Transcript lengths can then be determined from the peaks in those profiles. The method is essentially a Northern blot in reverse: instead of a gene probe labeled and hybridized to size-separated RNA immobilized on a membrane, size-separated RNA is labeled and hybridized to gene probes immobilized on a glass slide.


Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae.

Hurowitz EH, Brown PO - Genome Biol. (2003)

Virtual Northern scheme.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC395734&req=5

Figure 1: Virtual Northern scheme.
Mentions: The Virtual Northern scheme is summarized in Figure 1. Poly(A) RNA is separated by length on an agarose gel. The gel is sliced into a large number of thin slices, each of which contains RNAs from a narrow range of lengths [8]. RNA from each slice is then recovered, fluorescently labeled, and hybridized to a separate DNA microarray. Systematic analysis of the variation in the hybridization signal - across the series of gel slices for each DNA sequence represented on the microarrays - gives the length profile of all the transcripts that contain that sequence (Figure 2). Transcript lengths can then be determined from the peaks in those profiles. The method is essentially a Northern blot in reverse: instead of a gene probe labeled and hybridized to size-separated RNA immobilized on a membrane, size-separated RNA is labeled and hybridized to gene probes immobilized on a glass slide.

Bottom Line: We found a close linear relationship between mRNA lengths and the lengths of known or predicted translated sequences; mRNAs were typically around 300 nucleotides longer than the translated sequences.Interestingly, we found that systematic differences in the total length of the untranslated sequences in mRNAs were related to the functions of the encoded proteins.A systematic relationship between the lengths of the untranslated regions in yeast mRNAs and the functions of the proteins they encode may point to an important regulatory role for these sequences.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA.

ABSTRACT

Background: Although the protein-coding sequences in the Saccharomyces cerevisiae genome have been studied and annotated extensively, much less is known about the extent and characteristics of the untranslated regions of yeast mRNAs.

Results: We developed a 'Virtual Northern' method, using DNA microarrays for genome-wide systematic analysis of mRNA lengths. We used this method to measure mRNAs corresponding to 84% of the annotated open reading frames (ORFs) in the S. cerevisiae genome, with high precision and accuracy (measurement errors +/- 6-7%). We found a close linear relationship between mRNA lengths and the lengths of known or predicted translated sequences; mRNAs were typically around 300 nucleotides longer than the translated sequences. Analysis of genes deviating from that relationship identified ORFs with annotation errors, ORFs that appear not to be bona fide genes, and potentially novel genes. Interestingly, we found that systematic differences in the total length of the untranslated sequences in mRNAs were related to the functions of the encoded proteins.

Conclusions: The Virtual Northern method provides a practical and efficient method for genome-scale analysis of transcript lengths. Approximately 12-15% of the yeast genome is represented in untranslated sequences of mRNAs. A systematic relationship between the lengths of the untranslated regions in yeast mRNAs and the functions of the proteins they encode may point to an important regulatory role for these sequences.

Show MeSH
Related in: MedlinePlus