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. 2005 Jun 16:6:93.
doi: 10.1186/1471-2164-6-93.

Evidence for abundant transcription of non-coding regions in the Saccharomyces cerevisiae genome

Moshe Havilio  1 , Erez Y Levanon, Galia Lerman, Martin Kupiec, Eli Eisenberg
Affiliations

Evidence for abundant transcription of non-coding regions in the Saccharomyces cerevisiae genome

Moshe Havilio et al. BMC Genomics. .

Abstract

Background: Recent studies in a growing number of organisms have yielded accumulating evidence that a significant portion of the non-coding region in the genome is transcribed. We address this issue in the yeast Saccharomyces cerevisiae.

Results: Taking into account the absence of a significantly large yeast EST database, we use microarray expression data collected for genomic regions erroneously believed to be coding to study the expression pattern of non-coding regions in the Saccharomyces cerevisiae genome. We find that at least 164 out of 589 (28%) such regions are expressed under specific biological conditions. In particular, looking at the probes that are located opposing other known genes at the same genomic locus, we find that 88 out of 341 (26%) of these genes support antisense transcription. The expression patterns of these antisense genes are positively correlated. We validate these results using RT-PCR on a sample of 6 non-coding transcripts.

Conclusion: 1. The yeast genome is transcribed on a scale larger than previously assumed. 2. Correlated transcription of antisense genes is abundant in the yeast genome. 3. Antisense genes in yeast are non-coding.

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Figures

Figure 1
Figure 1
Distributions of PC for S/AS DO/non-DO pairs (blue) and randomly reshuffled DO/non-DO pairs from the S/AS set (green). 103,479 pairs used to calculate the second distribution. There is a significant difference between the S/AS and random distribution (χ2 = 124, DF = 9 and P = 10-22). S/AS pairs are significantly more correlated than random DO/non-DO pairs. For the S/AS distribution average = 0.076 and SD = 0.22. For the reshuffled distribution average = -0.018 and SD = 0.18. The significance of the difference in the averages is Pt = 10-20 (student t-test).
Figure 2
Figure 2
RT-PCR analysis of dubious ORFs. A) Reverse-transcription was carried out using oligo dT and specific primers for each ORF. RT: reverse transcription followed by PCR amplification. N: No reverse transcriptase added. G: Genomic DNA (positive control). NS: No RNA or DNA substrate added (negative control). B) A similar RT-PCR analysis was carried out for sense-antisense pairs. Shown here are YGR181w/TIM13 and the DO YGR182c. No amplification was detected with primers p1 and p4. If a transcript was present that encompasses both ORFs, amplification was expected, of the size observed in the reaction carried out with genomic DNA
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