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GC content of Early Metazoan genes and its impact on gene expression levels in mammalian cell lines

Ismail Sahin Gül (UGent) , Jens Staal (UGent) , Paco Hulpiau (UGent) , Evi De Keuckelaere (UGent) , Kai Kamm, Tom Deroo (UGent) , Ellen Sanders (UGent) , Katrien Staes (UGent) , Yasmine Driege (UGent) , Yvan Saeys (UGent) , et al.
(2018) GENOME BIOLOGY AND EVOLUTION. 10(3). p.909-917
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Abstract
With the genomes available for many animal clades, including the early-branching metazoans, one can readily study the functional conservation of genes across a diversity of animal lineages. Ectopic expression of an animal protein in, for instance, amammalian cell line is a generally used strategy in structure-function analysis. However, thismight turn out to be problematic in case of distantly related species. Here we analyzed the GC content of the coding sequences of basal animals and show its impact on gene expression levels in human cell lines, and, importantly, how this expression efficiency can be improved. Optimization of the GC3 content in the coding sequences of cadherin, alpha-catenin, and paracaspase of Trichoplax adhaerens dramatically increased the expression of these basal animal genes in human cell lines.
Keywords
TRICHOPLAX-ADHAERENS, HUMAN GENOME, EVOLUTION, SELECTION, SITES, ORGANIZATION, COMPLEXITY, ISOCHORES, CADHERINS, HISTORY, Trichoplax adhaerens, Placozoa, genome evolution, GC content, ectopic, expression

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MLA
Gül, Ismail Sahin et al. “GC Content of Early Metazoan Genes and Its Impact on Gene Expression Levels in Mammalian Cell Lines.” GENOME BIOLOGY AND EVOLUTION 10.3 (2018): 909–917. Print.
APA
Gül, I. S., Staal, J., Hulpiau, P., De Keuckelaere, E., Kamm, K., Deroo, T., Sanders, E., et al. (2018). GC content of Early Metazoan genes and its impact on gene expression levels in mammalian cell lines. GENOME BIOLOGY AND EVOLUTION, 10(3), 909–917.
Chicago author-date
Gül, Ismail Sahin, Jens Staal, Paco Hulpiau, Evi De Keuckelaere, Kai Kamm, Tom Deroo, Ellen Sanders, et al. 2018. “GC Content of Early Metazoan Genes and Its Impact on Gene Expression Levels in Mammalian Cell Lines.” Genome Biology and Evolution 10 (3): 909–917.
Chicago author-date (all authors)
Gül, Ismail Sahin, Jens Staal, Paco Hulpiau, Evi De Keuckelaere, Kai Kamm, Tom Deroo, Ellen Sanders, Katrien Staes, Yasmine Driege, Yvan Saeys, Rudi Beyaert, Ulrich Technau, Bernd Schierwater, and Frans Van Roy. 2018. “GC Content of Early Metazoan Genes and Its Impact on Gene Expression Levels in Mammalian Cell Lines.” Genome Biology and Evolution 10 (3): 909–917.
Vancouver
1.
Gül IS, Staal J, Hulpiau P, De Keuckelaere E, Kamm K, Deroo T, et al. GC content of Early Metazoan genes and its impact on gene expression levels in mammalian cell lines. GENOME BIOLOGY AND EVOLUTION. 2018;10(3):909–17.
IEEE
[1]
I. S. Gül et al., “GC content of Early Metazoan genes and its impact on gene expression levels in mammalian cell lines,” GENOME BIOLOGY AND EVOLUTION, vol. 10, no. 3, pp. 909–917, 2018.
@article{8561364,
  abstract     = {With the genomes available for many animal clades, including the early-branching metazoans, one can readily study the functional conservation of genes across a diversity of animal lineages. Ectopic expression of an animal protein in, for instance, amammalian cell line is a generally used strategy in structure-function analysis. However, thismight turn out to be problematic in case of distantly related species. Here we analyzed the GC content of the coding sequences of basal animals and show its impact on gene expression levels in human cell lines, and, importantly, how this expression efficiency can be improved. Optimization of the GC3 content in the coding sequences of cadherin, alpha-catenin, and paracaspase of Trichoplax adhaerens dramatically increased the expression of these basal animal genes in human cell lines.},
  author       = {Gül, Ismail Sahin and Staal, Jens and Hulpiau, Paco and De Keuckelaere, Evi and Kamm, Kai and Deroo, Tom and Sanders, Ellen and Staes, Katrien and Driege, Yasmine and Saeys, Yvan and Beyaert, Rudi and Technau, Ulrich and Schierwater, Bernd and Van Roy, Frans},
  issn         = {1759-6653},
  journal      = {GENOME BIOLOGY AND EVOLUTION},
  keywords     = {TRICHOPLAX-ADHAERENS,HUMAN GENOME,EVOLUTION,SELECTION,SITES,ORGANIZATION,COMPLEXITY,ISOCHORES,CADHERINS,HISTORY,Trichoplax adhaerens,Placozoa,genome evolution,GC content,ectopic,expression},
  language     = {eng},
  number       = {3},
  pages        = {909--917},
  title        = {GC content of Early Metazoan genes and its impact on gene expression levels in mammalian cell lines},
  url          = {http://dx.doi.org/10.1093/gbe/evy040},
  volume       = {10},
  year         = {2018},
}

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