Parallel Evolution of Chromatin Structure Underlying Metabolic Adaptation
(2017) In Molecular biology and evolution 34(11). p.2870-2878- Abstract
Parallel evolution occurs when a similar trait emerges in independent evolutionary lineages. Although changes in protein coding and gene transcription have been investigated as underlying mechanisms for parallel evolution, parallel changes in chromatin structure have never been reported. Here, Saccharomyces cerevisiae and a distantly related yeast species, Dekkera bruxellensis, are investigated because both species have independently evolved the capacity of aerobic fermentation. By profiling and comparing genome sequences, transcriptomic landscapes, and chromatin structures, we revealed that parallel changes in nucleosome occupancy in the promoter regions of mitochondria-localized genes led to concerted suppression of mitochondrial... (More)
Parallel evolution occurs when a similar trait emerges in independent evolutionary lineages. Although changes in protein coding and gene transcription have been investigated as underlying mechanisms for parallel evolution, parallel changes in chromatin structure have never been reported. Here, Saccharomyces cerevisiae and a distantly related yeast species, Dekkera bruxellensis, are investigated because both species have independently evolved the capacity of aerobic fermentation. By profiling and comparing genome sequences, transcriptomic landscapes, and chromatin structures, we revealed that parallel changes in nucleosome occupancy in the promoter regions of mitochondria-localized genes led to concerted suppression of mitochondrial functions by glucose, which can explain the metabolic convergence in these two independent yeast species. Further investigation indicated that similar mutational processes in the promoter regions of these genes in the two independent evolutionary lineages underlay the parallel changes in chromatin structure. Our results indicate that, despite several hundred million years of separation, parallel changes in chromatin structure, can be an important adaptation mechanism for different organisms. Due to the important role of chromatin structure changes in regulating gene expression and organism phenotypes, the novel mechanism revealed in this study could be a general phenomenon contributing to parallel adaptation in nature.
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- author
- Cheng, Jian ; Guo, Xiaoxian ; Cai, Pengli ; Cheng, Xiaozhi ; Piškur, Jure LU ; Ma, Yanhe ; Jiang, Huifeng and Gu, Zhenglong
- organization
- publishing date
- 2017-11-01
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- aerobic fermentation, chromatin, gene regulation evolution, parallel evolution
- in
- Molecular biology and evolution
- volume
- 34
- issue
- 11
- pages
- 9 pages
- publisher
- Oxford University Press
- external identifiers
-
- scopus:85044107257
- pmid:28961859
- ISSN
- 0737-4038
- DOI
- 10.1093/molbev/msx220
- language
- English
- LU publication?
- yes
- id
- b245cc77-8f75-406e-bf59-d6dab6507cd7
- date added to LUP
- 2018-04-10 14:05:09
- date last changed
- 2025-01-08 08:09:01
@article{b245cc77-8f75-406e-bf59-d6dab6507cd7,
abstract = {{<p>Parallel evolution occurs when a similar trait emerges in independent evolutionary lineages. Although changes in protein coding and gene transcription have been investigated as underlying mechanisms for parallel evolution, parallel changes in chromatin structure have never been reported. Here, Saccharomyces cerevisiae and a distantly related yeast species, Dekkera bruxellensis, are investigated because both species have independently evolved the capacity of aerobic fermentation. By profiling and comparing genome sequences, transcriptomic landscapes, and chromatin structures, we revealed that parallel changes in nucleosome occupancy in the promoter regions of mitochondria-localized genes led to concerted suppression of mitochondrial functions by glucose, which can explain the metabolic convergence in these two independent yeast species. Further investigation indicated that similar mutational processes in the promoter regions of these genes in the two independent evolutionary lineages underlay the parallel changes in chromatin structure. Our results indicate that, despite several hundred million years of separation, parallel changes in chromatin structure, can be an important adaptation mechanism for different organisms. Due to the important role of chromatin structure changes in regulating gene expression and organism phenotypes, the novel mechanism revealed in this study could be a general phenomenon contributing to parallel adaptation in nature.</p>}},
author = {{Cheng, Jian and Guo, Xiaoxian and Cai, Pengli and Cheng, Xiaozhi and Piškur, Jure and Ma, Yanhe and Jiang, Huifeng and Gu, Zhenglong}},
issn = {{0737-4038}},
keywords = {{aerobic fermentation; chromatin; gene regulation evolution; parallel evolution}},
language = {{eng}},
month = {{11}},
number = {{11}},
pages = {{2870--2878}},
publisher = {{Oxford University Press}},
series = {{Molecular biology and evolution}},
title = {{Parallel Evolution of Chromatin Structure Underlying Metabolic Adaptation}},
url = {{http://dx.doi.org/10.1093/molbev/msx220}},
doi = {{10.1093/molbev/msx220}},
volume = {{34}},
year = {{2017}},
}