The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses
Identifieur interne : 001B59 ( Main/Exploration ); précédent : 001B58; suivant : 001B60The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses
Auteurs : Tuan On [Canada] ; Xuejian Xiong [Canada] ; Shuye Pu [Canada] ; Andrei Turinsky [Canada] ; Yunchen Gong [Canada] ; Andrew Emili [Canada] ; Zhaolei Zhang [Canada] ; Jack Greenblatt [Canada] ; Shoshana J. Wodak [Canada] ; John Parkinson [Canada]Source :
- Proteins: Structure, Function, and Bioinformatics [ 0887-3585 ] ; 2010-07.
English descriptors
- KwdEn :
- Animals, Caenorhabditis elegans, Chromatin (genetics), Chromatin Assembly and Disassembly (genetics), Cluster Analysis, Computational Biology (methods), Drosophila melanogaster, Eukaryota, Evolution, Molecular, Gene Regulatory Networks, Humans, Models, Genetic, Phylogeny, Protein Interaction Mapping (methods), Saccharomyces cerevisiae, bioinformatics, biological systems, chromatin modification, epigenetics, evolutionary trajectory, phylogenomics, protein–protein interactions.
- MESH :
- chemical , genetics : Chromatin.
- genetics : Chromatin Assembly and Disassembly.
- methods : Computational Biology, Protein Interaction Mapping.
- Animals, Caenorhabditis elegans, Cluster Analysis, Drosophila melanogaster, Eukaryota, Evolution, Molecular, Gene Regulatory Networks, Humans, Models, Genetic, Phylogeny, Saccharomyces cerevisiae.
Abstract
Model organisms such as yeast, fly, and worm have played a defining role in the study of many biological systems. A significant challenge remains in translating this information to humans. Of critical importance is the ability to differentiate those components where knowledge of function and interactions may be reliably inferred from those that represent lineage‐specific innovations. To address this challenge, we use chromatin modification (CM) as a model system for exploring the evolutionary properties of their components in the context of their known functions and interactions. Collating previously identified components of CM from yeast, worm, fly, and human, we identified a “core” set of 50 CM genes displaying consistent orthologous relationships that likely retain their interactions and functions across taxa. In addition, we catalog many components that demonstrate lineage specific expansions and losses, highlighting much duplication within vertebrates that may reflect an expanded repertoire of regulatory mechanisms. Placed in the context of a high‐quality protein–protein interaction network, we find, contrary to existing views of evolutionary modularity, that CM complex components display a mosaic of evolutionary histories: a core set of highly conserved genes, together with sets displaying lineage specific innovations. Although focused on CM, this study provides a template for differentiating those genes which are likely to retain their functions and interactions across species. As such, in addition to informing on the evolution of CM as a system, this study provides a set of comparative genomic approaches that can be generally applied to any biological systems. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Url:
DOI: 10.1002/prot.22723
Affiliations:
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sort="Zhang, Zhaolei" uniqKey="Zhang Z" first="Zhaolei" last="Zhang">Zhaolei Zhang</name><affiliation wicri:level="4"><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Molecular Genetics, University of Toronto, Toronto, Ontario</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation><affiliation wicri:level="4"><country>Canada</country><wicri:regionArea>Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation><affiliation wicri:level="4"><country>Canada</country><wicri:regionArea>Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, 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sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name><affiliation wicri:level="1"><country xml:lang="fr">Canada</country><wicri:regionArea>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario</wicri:regionArea><wicri:noRegion>Ontario</wicri:noRegion></affiliation><affiliation wicri:level="4"><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Molecular Genetics, University of Toronto, Toronto, Ontario</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation><affiliation wicri:level="4"><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Biochemistry, University of Toronto, Toronto, Ontario</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation><affiliation wicri:level="1"><country>Canada</country><wicri:regionArea>Molecular Structure and Function, Hospital for Sick Children, Toronto Medical Discovery Tower (East), 15th Floor, RM 15‐704, 101 College Street, Toronto, ON</wicri:regionArea><wicri:noRegion>ON</wicri:noRegion></affiliation></author></analytic><monogr></monogr><series><title level="j">Proteins: Structure, Function, and Bioinformatics</title><title level="j" type="abbrev">Proteins</title><idno type="ISSN">0887-3585</idno><idno type="eISSN">1097-0134</idno><imprint><publisher>Wiley Subscription Services, Inc., A Wiley Company</publisher><pubPlace>Hoboken</pubPlace><date type="published" when="2010-07">2010-07</date><biblScope unit="volume">78</biblScope><biblScope unit="issue">9</biblScope><biblScope unit="page" from="2075">2075</biblScope><biblScope unit="page" to="2089">2089</biblScope></imprint><idno type="ISSN">0887-3585</idno></series><idno type="istex">5E85F0537370B92AA35C4C9B9D6C0D6071FD8BA8</idno><idno type="DOI">10.1002/prot.22723</idno><idno type="ArticleID">PROT22723</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0887-3585</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Caenorhabditis elegans</term><term>Chromatin (genetics)</term><term>Chromatin Assembly and Disassembly (genetics)</term><term>Cluster Analysis</term><term>Computational Biology (methods)</term><term>Drosophila melanogaster</term><term>Eukaryota</term><term>Evolution, Molecular</term><term>Gene Regulatory Networks</term><term>Humans</term><term>Models, Genetic</term><term>Phylogeny</term><term>Protein Interaction Mapping (methods)</term><term>Saccharomyces cerevisiae</term><term>bioinformatics</term><term>biological systems</term><term>chromatin modification</term><term>epigenetics</term><term>evolutionary trajectory</term><term>phylogenomics</term><term>protein–protein interactions</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Chromatin</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chromatin Assembly and Disassembly</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term><term>Protein Interaction Mapping</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Caenorhabditis elegans</term><term>Cluster Analysis</term><term>Drosophila melanogaster</term><term>Eukaryota</term><term>Evolution, Molecular</term><term>Gene Regulatory Networks</term><term>Humans</term><term>Models, Genetic</term><term>Phylogeny</term><term>Saccharomyces cerevisiae</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Model organisms such as yeast, fly, and worm have played a defining role in the study of many biological systems. A significant challenge remains in translating this information to humans. Of critical importance is the ability to differentiate those components where knowledge of function and interactions may be reliably inferred from those that represent lineage‐specific innovations. To address this challenge, we use chromatin modification (CM) as a model system for exploring the evolutionary properties of their components in the context of their known functions and interactions. Collating previously identified components of CM from yeast, worm, fly, and human, we identified a “core” set of 50 CM genes displaying consistent orthologous relationships that likely retain their interactions and functions across taxa. In addition, we catalog many components that demonstrate lineage specific expansions and losses, highlighting much duplication within vertebrates that may reflect an expanded repertoire of regulatory mechanisms. Placed in the context of a high‐quality protein–protein interaction network, we find, contrary to existing views of evolutionary modularity, that CM complex components display a mosaic of evolutionary histories: a core set of highly conserved genes, together with sets displaying lineage specific innovations. Although focused on CM, this study provides a template for differentiating those genes which are likely to retain their functions and interactions across species. As such, in addition to informing on the evolution of CM as a system, this study provides a set of comparative genomic approaches that can be generally applied to any biological systems. Proteins 2010. © 2010 Wiley‐Liss, Inc.</div></front></TEI><affiliations><list><country><li>Canada</li></country><region><li>Ontario</li></region><settlement><li>Toronto</li></settlement><orgName><li>Université de Toronto</li></orgName></list><tree><country name="Canada"><noRegion><name sortKey="On, Tuan" sort="On, Tuan" uniqKey="On T" first="Tuan" last="On">Tuan On</name></noRegion><name sortKey="Emili, Andrew" sort="Emili, Andrew" uniqKey="Emili A" first="Andrew" last="Emili">Andrew Emili</name><name sortKey="Emili, Andrew" sort="Emili, Andrew" uniqKey="Emili A" first="Andrew" last="Emili">Andrew Emili</name><name sortKey="Emili, Andrew" sort="Emili, Andrew" uniqKey="Emili A" first="Andrew" last="Emili">Andrew Emili</name><name sortKey="Gong, Yunchen" sort="Gong, Yunchen" uniqKey="Gong Y" first="Yunchen" last="Gong">Yunchen Gong</name><name sortKey="Gong, Yunchen" sort="Gong, Yunchen" uniqKey="Gong Y" first="Yunchen" last="Gong">Yunchen Gong</name><name sortKey="Greenblatt, Jack" sort="Greenblatt, Jack" uniqKey="Greenblatt J" first="Jack" last="Greenblatt">Jack Greenblatt</name><name sortKey="Greenblatt, Jack" sort="Greenblatt, Jack" uniqKey="Greenblatt J" first="Jack" last="Greenblatt">Jack Greenblatt</name><name sortKey="Greenblatt, Jack" sort="Greenblatt, Jack" uniqKey="Greenblatt J" first="Jack" last="Greenblatt">Jack Greenblatt</name><name sortKey="On, Tuan" sort="On, Tuan" uniqKey="On T" first="Tuan" last="On">Tuan On</name><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name><name sortKey="Pu, Shuye" sort="Pu, Shuye" uniqKey="Pu S" first="Shuye" last="Pu">Shuye Pu</name><name sortKey="Turinsky, Andrei" sort="Turinsky, Andrei" uniqKey="Turinsky A" first="Andrei" last="Turinsky">Andrei Turinsky</name><name sortKey="Wodak, Shoshana J" sort="Wodak, Shoshana J" uniqKey="Wodak S" first="Shoshana J." last="Wodak">Shoshana J. Wodak</name><name sortKey="Wodak, Shoshana J" sort="Wodak, Shoshana J" uniqKey="Wodak S" first="Shoshana J." last="Wodak">Shoshana J. Wodak</name><name sortKey="Wodak, Shoshana J" sort="Wodak, Shoshana J" uniqKey="Wodak S" first="Shoshana J." last="Wodak">Shoshana J. Wodak</name><name sortKey="Xiong, Xuejian" sort="Xiong, Xuejian" uniqKey="Xiong X" first="Xuejian" last="Xiong">Xuejian Xiong</name><name sortKey="Zhang, Zhaolei" sort="Zhang, Zhaolei" uniqKey="Zhang Z" first="Zhaolei" last="Zhang">Zhaolei Zhang</name><name sortKey="Zhang, Zhaolei" sort="Zhang, Zhaolei" uniqKey="Zhang Z" first="Zhaolei" last="Zhang">Zhaolei Zhang</name><name sortKey="Zhang, Zhaolei" sort="Zhang, Zhaolei" uniqKey="Zhang Z" first="Zhaolei" last="Zhang">Zhaolei Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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