Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species
Background Recent studies in budding yeast have shown that antisense transcription occurs at many loci. However, the functional role of antisense transcripts has been demonstrated only in a few cases and it has been suggested that most antisense transcripts may result from promiscuous bi-directio...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | en_US |
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Springer (Biomed Central Ltd.)
2012
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| Online Access: | http://hdl.handle.net/1721.1/69638 https://orcid.org/0000-0001-8567-2049 |
| _version_ | 1811077593779142656 |
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| author | Yassour, Moran Pfiffner, Jenna Levin, Joshua Z. Adiconis, Xian Gnirke, Andreas Nusbaum, Chad Thompson, Dawn-Anne Friedman, Nir Regev, Aviv Yassour, Moran |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Yassour, Moran Pfiffner, Jenna Levin, Joshua Z. Adiconis, Xian Gnirke, Andreas Nusbaum, Chad Thompson, Dawn-Anne Friedman, Nir Regev, Aviv Yassour, Moran |
| author_sort | Yassour, Moran |
| collection | MIT |
| description | Background
Recent studies in budding yeast have shown that antisense transcription occurs at many loci. However, the functional role of antisense transcripts has been demonstrated only in a few cases and it has been suggested that most antisense transcripts may result from promiscuous bi-directional transcription in a dense genome.
Results
Here, we use strand-specific RNA sequencing to study anti-sense transcription in Saccharomyces cerevisiae. We detect 1,103 putative antisense transcripts expressed in mid-log phase growth, ranging from 39 short transcripts covering only the 3' UTR of sense genes to 145 long transcripts covering the entire sense open reading frame. Many of these antisense transcripts overlap sense genes that are repressed in mid-log phase and are important in stationary phase, stress response, or meiosis. We validate the differential regulation of 67 antisense transcripts and their sense targets in relevant conditions, including nutrient limitation and environmental stresses. Moreover, we show that several antisense transcripts and, in some cases, their differential expression have been conserved across five species of yeast spanning 150 million years of evolution. Divergence in the regulation of antisense transcripts to two respiratory genes coincides with the evolution of respiro-fermentation.
Conclusions
Our work provides support for a global and conserved role for antisense transcription in yeast gene regulation. |
| first_indexed | 2024-09-23T10:45:29Z |
| format | Article |
| id | mit-1721.1/69638 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:45:29Z |
| publishDate | 2012 |
| publisher | Springer (Biomed Central Ltd.) |
| record_format | dspace |
| spelling | mit-1721.1/696382022-09-30T22:46:03Z Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species Yassour, Moran Pfiffner, Jenna Levin, Joshua Z. Adiconis, Xian Gnirke, Andreas Nusbaum, Chad Thompson, Dawn-Anne Friedman, Nir Regev, Aviv Yassour, Moran Massachusetts Institute of Technology. Department of Biology Regev, Aviv Friedman, Nir Regev, Aviv Yassour, Moran Background Recent studies in budding yeast have shown that antisense transcription occurs at many loci. However, the functional role of antisense transcripts has been demonstrated only in a few cases and it has been suggested that most antisense transcripts may result from promiscuous bi-directional transcription in a dense genome. Results Here, we use strand-specific RNA sequencing to study anti-sense transcription in Saccharomyces cerevisiae. We detect 1,103 putative antisense transcripts expressed in mid-log phase growth, ranging from 39 short transcripts covering only the 3' UTR of sense genes to 145 long transcripts covering the entire sense open reading frame. Many of these antisense transcripts overlap sense genes that are repressed in mid-log phase and are important in stationary phase, stress response, or meiosis. We validate the differential regulation of 67 antisense transcripts and their sense targets in relevant conditions, including nutrient limitation and environmental stresses. Moreover, we show that several antisense transcripts and, in some cases, their differential expression have been conserved across five species of yeast spanning 150 million years of evolution. Divergence in the regulation of antisense transcripts to two respiratory genes coincides with the evolution of respiro-fermentation. Conclusions Our work provides support for a global and conserved role for antisense transcription in yeast gene regulation. Canadian Friends of the Hebrew University Howard Hughes Medical Institute Human Frontier Science Program (Strasbourg, France) Burroughs Wellcome Fund (Career Award at the Scientific Interface) National Institutes of Health (U.S.). Pioneer Award Broad Institute of MIT and Harvard U.S.-Israel Binational Science Foundation (BSF) National Human Genome Research Institute (U.S.) Alfred P. Sloan Foundation 2012-03-09T20:05:41Z 2012-03-09T20:05:41Z 2010-08 2010-07 Article http://purl.org/eprint/type/JournalArticle 1465-6906 1474-7596 http://hdl.handle.net/1721.1/69638 Yassour, Moran et al. “Strand-specific RNA Sequencing Reveals Extensive Regulated Long Antisense Transcripts That Are Conserved Across Yeast Species.” Genome Biology 11.8 (2010): R87. Web. 9 Mar. 2012. https://orcid.org/0000-0001-8567-2049 en_US http://dx.doi.org/10.1186/gb-2010-11-8-r87 Genome Biology Creative Commons Attribution http://creativecommons.org/licenses/by/2.0 application/pdf Springer (Biomed Central Ltd.) BioMed Central |
| spellingShingle | Yassour, Moran Pfiffner, Jenna Levin, Joshua Z. Adiconis, Xian Gnirke, Andreas Nusbaum, Chad Thompson, Dawn-Anne Friedman, Nir Regev, Aviv Yassour, Moran Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species |
| title | Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species |
| title_full | Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species |
| title_fullStr | Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species |
| title_full_unstemmed | Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species |
| title_short | Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species |
| title_sort | strand specific rna sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species |
| url | http://hdl.handle.net/1721.1/69638 https://orcid.org/0000-0001-8567-2049 |
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