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Parallel Evolution of Chromatin Structure Underlying Metabolic Adaptation

Cheng, Jian ; Guo, Xiaoxian ; Cai, Pengli ; Cheng, Xiaozhi ; Piškur, Jure LU ; Ma, Yanhe ; Jiang, Huifeng and Gu, Zhenglong (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
organization
publishing date
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
  • pmid:28961859
  • scopus:85044107257
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
2020-07-01 04:32:27
@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},
  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},
}