The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses

被引:13
作者
On, Tuan [1 ,2 ]
Xiong, Xuejian [1 ]
Pu, Shuye [1 ]
Turinsky, Andrei [1 ]
Gong, Yunchen [3 ,4 ]
Emili, Andrew [2 ,3 ,4 ]
Zhang, Zhaolei [2 ,3 ,4 ]
Greenblatt, Jack [2 ,3 ,4 ]
Wodak, Shoshana J. [1 ,2 ,5 ]
Parkinson, John [1 ,2 ,5 ]
机构
[1] Hosp Sick Children, Program Mol Struct & Funct, Toronto, ON M5G 1L7, Canada
[2] Univ Toronto, Dept Mol Genet, Toronto, ON, Canada
[3] Univ Toronto, Banting & Best Dept Med Res, Toronto, ON M5S 3E1, Canada
[4] Univ Toronto, Terrence Donnelly Ctr Cellular & Biomol Res, Toronto, ON M5S 3E1, Canada
[5] Univ Toronto, Dept Biochem, Toronto, ON, Canada
基金
加拿大健康研究院; 加拿大自然科学与工程研究理事会;
关键词
chromatin modification; bioinformatics; protein-protein interactions; phylogenomics; epigenetics; evolutionary trajectory; biological systems; TRANSCRIPTION FACTORS; HISTONE ACETYLATION; COMPLEXES; ACETYLTRANSFERASE; IDENTIFICATION; NETWORKS; PARASITE; DEACETYLATION; METHYLATION; GENOMICS;
D O I
10.1002/prot.22723
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:2075 / 2089
页数:15
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