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| Status |
Public on Nov 10, 2013 |
| Title |
Inheritance of gene expression level and selective constraints on trans- and cis-regulatory changes in yeast |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Gene expression evolution can be caused by changes in cis- or trans-regulatory elements or both. As cis and trans regulation operate through different molecular mechanisms, cis and trans mutations may show different inheritance patterns and may be subjected to different selective constraints. To investigate these issues, we obtained and analyzed gene expression data from two Saccharomyces cerevisiae strains and their hybrid, using high-throughput sequencing. Our data indicate that compared to other types of genes, those with antagonistic cis-trans interactions are more likely to exhibit over- or under-dominant inheritance of expression level. Moreover, in accordance with previous studies, genes with trans variants tend to have a dominant inheritance pattern while cis variants are enriched for additive inheritance. In addition, cis regulatory differences contribute more to expression differences between species than within species, whereas trans regulatory differences show a stronger association between divergence and polymorphism. Our data indicate that in the trans component of gene expression differences genes subjected to weaker selective constraints tend to have an excess of polymorphism over divergence compared to those subjected to stronger selective constraints. In contrast, in the cis component, this difference between genes under stronger and weaker selective constraint is mostly absent. To explain these observations, we propose that purifying selection more strongly shapes trans polymorphism than cis polymorphism.
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| Overall design |
Study the gene expression patterns in two strains of yeast (BY and RM)
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| Contributor(s) |
Li W, Schaefke B, Emerson JJ, Wang T, Lu MJ, Hsieh L |
| Citation(s) |
23793114 |
| BioProject |
PRJNA194385 |
| Submission date |
May 10, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Li-Ching Hsieh |
| Organization name |
Academia Sinica
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| Department |
Biodiversity Research Center
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| Lab |
Li Lab
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| Street address |
128 Academia Road, Section 2
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| City |
Taipei |
| ZIP/Postal code |
115 |
| Country |
Taiwan |
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| Platforms (1) |
| GPL13272 |
Illumina Genome Analyzer IIx (Saccharomyces cerevisiae) |
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| Samples (4)
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| Relations |
| SRA |
SRP022356 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE46838_RAW.tar |
120.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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