Evolutionary principles of modular gene regulation in yeasts
Divergence in gene regulation can play a major role in evolution. Here, we used a phylogenetic framework to measure mRNA profiles in 15 yeast species from the phylum Ascomycota and reconstruct the evolution of their modular regulatory programs along a time course of growth on glucose over 300 millio...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications Ltd
2013-06-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/00603 |
| _version_ | 1818028311340646400 |
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| author | Dawn A Thompson Sushmita Roy Michelle Chan Mark P Styczynsky Jenna Pfiffner Courtney French Amanda Socha Anne Thielke Sara Napolitano Paul Muller Manolis Kellis Jay H Konieczka Ilan Wapinski Aviv Regev |
| author_facet | Dawn A Thompson Sushmita Roy Michelle Chan Mark P Styczynsky Jenna Pfiffner Courtney French Amanda Socha Anne Thielke Sara Napolitano Paul Muller Manolis Kellis Jay H Konieczka Ilan Wapinski Aviv Regev |
| author_sort | Dawn A Thompson |
| collection | DOAJ |
| description | Divergence in gene regulation can play a major role in evolution. Here, we used a phylogenetic framework to measure mRNA profiles in 15 yeast species from the phylum Ascomycota and reconstruct the evolution of their modular regulatory programs along a time course of growth on glucose over 300 million years. We found that modules have diverged proportionally to phylogenetic distance, with prominent changes in gene regulation accompanying changes in lifestyle and ploidy, especially in carbon metabolism. Paralogs have significantly contributed to regulatory divergence, typically within a very short window from their duplication. Paralogs from a whole genome duplication (WGD) event have a uniquely substantial contribution that extends over a longer span. Similar patterns occur when considering the evolution of the heat shock regulatory program measured in eight of the species, suggesting that these are general evolutionary principles. |
| first_indexed | 2024-12-10T05:01:47Z |
| format | Article |
| id | doaj.art-6c41a8412cae4405bcabcd5acc8a0273 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-12-10T05:01:47Z |
| publishDate | 2013-06-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-6c41a8412cae4405bcabcd5acc8a02732022-12-22T02:01:23ZengeLife Sciences Publications LtdeLife2050-084X2013-06-01210.7554/eLife.00603Evolutionary principles of modular gene regulation in yeastsDawn A Thompson0Sushmita Roy1Michelle Chan2Mark P Styczynsky3Jenna Pfiffner4Courtney French5Amanda Socha6Anne Thielke7Sara Napolitano8Paul Muller9Manolis Kellis10Jay H Konieczka11Ilan Wapinski12Aviv Regev13Broad Institute of MIT and Harvard, Cambridge, United StatesBroad Institute of MIT and Harvard, Cambridge, United States; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, United StatesBroad Institute of MIT and Harvard, Cambridge, United States; Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, United StatesBroad Institute of MIT and Harvard, Cambridge, United StatesBroad Institute of MIT and Harvard, Cambridge, United StatesBroad Institute of MIT and Harvard, Cambridge, United StatesBroad Institute of MIT and Harvard, Cambridge, United StatesBroad Institute of MIT and Harvard, Cambridge, United StatesBroad Institute of MIT and Harvard, Cambridge, United StatesBroad Institute of MIT and Harvard, Cambridge, United StatesComputer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, United StatesBroad Institute of MIT and Harvard, Cambridge, United StatesBroad Institute of MIT and Harvard, Cambridge, United StatesBroad Institute of MIT and Harvard, Cambridge, United States; Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United StatesDivergence in gene regulation can play a major role in evolution. Here, we used a phylogenetic framework to measure mRNA profiles in 15 yeast species from the phylum Ascomycota and reconstruct the evolution of their modular regulatory programs along a time course of growth on glucose over 300 million years. We found that modules have diverged proportionally to phylogenetic distance, with prominent changes in gene regulation accompanying changes in lifestyle and ploidy, especially in carbon metabolism. Paralogs have significantly contributed to regulatory divergence, typically within a very short window from their duplication. Paralogs from a whole genome duplication (WGD) event have a uniquely substantial contribution that extends over a longer span. Similar patterns occur when considering the evolution of the heat shock regulatory program measured in eight of the species, suggesting that these are general evolutionary principles.https://elifesciences.org/articles/00603regulatory evolutionduplicationdivergencecarbon lifestylemodulegene expression |
| spellingShingle | Dawn A Thompson Sushmita Roy Michelle Chan Mark P Styczynsky Jenna Pfiffner Courtney French Amanda Socha Anne Thielke Sara Napolitano Paul Muller Manolis Kellis Jay H Konieczka Ilan Wapinski Aviv Regev Evolutionary principles of modular gene regulation in yeasts eLife regulatory evolution duplication divergence carbon lifestyle module gene expression |
| title | Evolutionary principles of modular gene regulation in yeasts |
| title_full | Evolutionary principles of modular gene regulation in yeasts |
| title_fullStr | Evolutionary principles of modular gene regulation in yeasts |
| title_full_unstemmed | Evolutionary principles of modular gene regulation in yeasts |
| title_short | Evolutionary principles of modular gene regulation in yeasts |
| title_sort | evolutionary principles of modular gene regulation in yeasts |
| topic | regulatory evolution duplication divergence carbon lifestyle module gene expression |
| url | https://elifesciences.org/articles/00603 |
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