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

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.

SUBMITTER: Havilio M

PROVIDER: S-EPMC1181813 | biostudies-other | 2005

REPOSITORIES: biostudies-other

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

Havilio Moshe M Levanon Erez Y EY Lerman Galia G Kupiec Martin M Eisenberg Eli E

BMC genomics 20050616

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

PMID: 15960846

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Project description:Cmr1 (changed mutation rate 1) is a largely uncharacterized nuclear protein that has recently emerged in several global genetic interaction and protein localization studies. It clusters with proteins involved in DNA damage and replication stress response, suggesting a role in maintaining genome integrity. Under conditions of proteasome inhibition or replication stress, this protein localizes to distinct sub-nuclear foci termed as intranuclear quality control (INQ) compartments, which sequester proteins for their subsequent degradation. Interestingly, it also interacts with histones, chromatin remodelers and modifiers, as well as with proteins involved in transcription including subunits of RNA Pol I and Pol III, but not with those of Pol II. It is not known whether Cmr1 plays a role in regulating transcription of Pol II target genes. Here, we show that Cmr1 is recruited to the coding regions of transcribed genes of S. cerevisiae. Cmr1 occupancy correlates with the Pol II occupancy genome-wide, indicating that it is recruited to coding sequences in a transcription-dependent manner. Cmr1-enriched genes include Gcn4 targets and ribosomal protein genes. Furthermore, our results show that Cmr1 recruitment to coding sequences is stimulated by Pol II CTD kinase, Kin28, and the histone deacetylases, Rpd3 and Hos2. Finally, our genome-wide analyses implicate Cmr1 in regulating Pol II occupancy at transcribed coding sequences. However, it is dispensable for maintaining co-transcriptional histone occupancy and histone modification (acetylation and methylation). Collectively, our results show that Cmr1 facilitates transcription by directly engaging with transcribed coding regions. ChIp-chip experiments were perfomed to determine genome-wide distribution of Cmr1 in WT and gcn4Î cells (S. cerevisiae). Rpb3 occupancy in WT and cmr1Î cells was also determined to reveal the changes in Pol II occupancy in the absence of Cmr1. The WT and mutant strains were grown in Synthetic complete and cells were indcued for Gcn4 by treating with Sulfometuron methyl for 30 minutes and processed for chromatin immunoprecipitation using antibodies against Myc and Rpb3 (subunit of Pol II).

Dataset Information

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

Publications

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

Similar Datasets

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