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Virtual northern using DNA microarrays for genome wide systematic analysis of mRNA lengths, used to measure mRNAs corresponding to 84% of the annotated open reading frames (ORFs) in the yeast genome

ABSTRACT: 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 1 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.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Janos Demeter

PROVIDER: E-SMDB-2508 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae.

Hurowitz Evan H EH Brown Patrick O PO

Genome biology 20031222 1

<h4>Background</h4>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.<h4>Results</h4>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 geno ...[more]

PMID: 14709174

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Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae

Project description: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 1 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. Groups of assays that are related as part of a time series. Computed

2005-12-29 | E-GEOD-3932 | biostudies-arrayexpress

Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae

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Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

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Virtual northern on human brain samples using DNA microarrays for systematic genome wide analysis of mRNA lengths

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