Guan Lab

Department of Computational Medicine & Bioinformatics
Thu, 01/16/2014 - 14:39 -- gyuanfan
TitleFunctional analysis of gene duplications in Saccharomyces cerevisiae.
Publication TypeJournal Article
Year of Publication2007
AuthorsGuan Y, Dunham MJ, Troyanskaya OG
JournalGenetics
Volume175
Issue2
Pagination933-43
Date Published2007 Feb
ISSN0016-6731
KeywordsBayes Theorem, Dosage Compensation, Genetic, Gene Duplication, Gene Expression Regulation, Fungal, Genes, Lethal, Genome, Fungal, Protein Binding, Regulatory Sequences, Nucleic Acid, Saccharomyces cerevisiae, Sequence Homology
Abstract

Gene duplication can occur on two scales: whole-genome duplications (WGD) and smaller-scale duplications (SSD) involving individual genes or genomic segments. Duplication may result in functionally redundant genes or diverge in function through neofunctionalization or subfunctionalization. The effect of duplication scale on functional evolution has not yet been explored, probably due to the lack of global knowledge of protein function and different times of duplication events. To address this question, we used integrated Bayesian analysis of diverse functional genomic data to accurately evaluate the extent of functional similarity and divergence between paralogs on a global scale. We found that paralogs resulting from the whole-genome duplication are more likely to share interaction partners and biological functions than smaller-scale duplicates, independent of sequence similarity. In addition, WGD paralogs show lower frequency of essential genes and higher synthetic lethality rate, but instead diverge more in expression pattern and upstream regulatory region. Thus, our analysis demonstrates that WGD paralogs generally have similar compensatory functions but diverging expression patterns, suggesting a potential of distinct evolutionary scenarios for paralogs that arose through different duplication mechanisms. Furthermore, by identifying these functional disparities between the two types of duplicates, we reconcile previous disputes on the relationship between sequence divergence and expression divergence or essentiality.

DOI10.1534/genetics.106.064329
Alternate JournalGenetics
PubMed ID17151249
PubMed Central IDPMC1800624
Grant ListR01 GM071966 / GM / NIGMS NIH HHS / United States