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Chromatin- and Transcription-Related Factors Repress Transcription from within Coding Regions throughout the Saccharomyces cerevisiae Genome

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Cheung, Vanessa, Chua, Gordon, Batada, Nizar N, Landry, Christian R, Michnick, Stephen W, Hughes, Timothy R, Winston, Fred·2008·PLoS Biology

DOI 10.1371/journal.pbio.0060277

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Abstract

Previous studies in Saccharomyces cerevisiae have demonstrated that cryptic promoters within coding regions activate transcription in particular mutants. We have performed a comprehensive analysis of cryptic transcription in order to identify factors that normally repress cryptic promoters, to determine the amount of cryptic transcription genome-wide, and to study the potential for expression of genetic information by cryptic transcription. Our results show that a large number of factors that control chromatin structure and transcription are required to repress cryptic transcription from at least 1,000 locations across the S. cerevisiae genome. Two results suggest that some cryptic transcripts are translated. First, as expected, many cryptic transcripts contain an ATG and an open reading frame of at least 100 codons. Second, several cryptic transcripts are translated into proteins. Furthermore, a subset of cryptic transcripts tested is transiently induced in wild-type cells following a nutritional shift, suggesting a possible physiological role in response to a change in growth conditions. Taken together, our results demonstrate that, during normal growth, the global integrity of gene expression is maintained by a wide range of factors and suggest that, under altered genetic or physiological conditions, the expression of alternative genetic information may occur.

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Duina, A. A., & Winston, F. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.24.2.561-572.2004 · Cited by 47
Self-citation
The undertranslated transcriptome reveals widespread translational silencing by alternative 5' transcript leaders
Law, G. L., Bickel, K. S., MacKay, V. L., & Morris, D. (2006) · Genome biology · doi:10.1186/gb-2005-6-13-r111 · Cited by 46
The Two Forms of Karyogamy Transcription Factor Kar4p Are Regulated by Differential Initiation of Transcription, Translation, and Protein Turnover
Gammie, A. E., Stewart, B. G., Scott, C. F., & Rose, M. D. (1999) · Molecular and Cellular Biology · doi:10.1128/mcb.19.1.817 · Cited by 42
Transcription reinitiation rate: A potential role for TATA box stabilization of the TFIID:TFIIA:DNA complex
Yean, D., & Gralla, J. D. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.3.831 · Cited by 37
Role of the Transcription Activator Ste12p as a Repressor of PRY3 Expression
Bickel, K. S., & Morris, D. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.01004-06 · Cited by 11

RNase H and Multiple RNA Biogenesis Factors Cooperate to Prevent RNA:DNA Hybrids from Generating Genome Instability
Wahba, L., Amon, J. D., Koshland, D., & Vuica-Ross, M. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.10.017 · Cited by 401
The Case for Junk DNA
Palazzo, A. F., & Gregory, T. R. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004351 · Cited by 279
Chromatin and Transcription in Yeast
Rando, O. J., & Winston, F. (2012) · Genetics · doi:10.1534/genetics.111.132266 · Cited by 269
Self-citation
Combinatorial complexity in chromatin structure and function: revisiting the histone code
Rando, O. J. (2012) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2012.02.013 · Cited by 269
H3K36 methylation promotes longevity by enhancing transcriptional fidelity
Sen, P., Dang, W., Donahue, G., Dai, J., Dorsey, J., Cao, X., Liu, W., Cao, K., Perry, R., Lee, J. Y., et al. (2015) · Genes & Development · doi:10.1101/gad.263707.115 · Cited by 233

See all 299

Authors: Cheung, V., Chua, G., Batada, N. N., Landry, C. R., Michnick, S. W., Hughes, T. R., & Winston, F.
Venue: PLoS Biology
Publisher: Public Library of Science (PLoS)
Published: 2008-11-11
Volume: 6
Issue: 11
Pages: e277
ISSN: 1544-9173 (ISSN-L)
1545-7885
DOI: 10.1371/journal.pbio.0060277
OpenAlex: W2162778315
Cited by: 299
References: 97
FWCI: 8.44
Type: journal article
Language: en
Open access: gold

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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.

Chromatin- and Transcription-Related Factors Repress Transcription from within Coding Regions throughout the Saccharomyces cerevisiae Genome

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