The evolution of human cells in terms of protein innovation

Sardar, Adam J., Oates, Mmatt E., Fang, Hai, Forrest, Alistair R. R., Kawaji, Hideya, The FANTOM Consortium, Gough, Julian and Rackham, Owen J. L. (2014) The evolution of human cells in terms of protein innovation. Molecular Biology and Evolution, 31 6: 1364-1374. doi:10.1093/molbev/mst139

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Author Sardar, Adam J.
Oates, Mmatt E.
Fang, Hai
Forrest, Alistair R. R.
Kawaji, Hideya
The FANTOM Consortium
Gough, Julian
Rackham, Owen J. L.
Title The evolution of human cells in terms of protein innovation
Journal name Molecular Biology and Evolution   Check publisher's open access policy
ISSN 0737-4038
Publication date 2014-06-01
Year available 2014
Sub-type Article (original research)
DOI 10.1093/molbev/mst139
Open Access Status DOI
Volume 31
Issue 6
Start page 1364
End page 1374
Total pages 11
Place of publication Cary, NC, United States
Publisher Oxford University Press
Language eng
Abstract Humans are composed of hundreds of cell types. As the genomic DNA of each somatic cell is identical, cell type is determined by what is expressed and when. Until recently, little has been reported about the determinants of human cell identity, particularly from the joint perspective of gene evolution and expression. Here, we chart the evolutionary past of all documented human cell types via the collective histories of proteins, the principal product of gene expression. FANTOM5 data provide cell-type–specific digital expression of human protein-coding genes and the SUPERFAMILY resource is used to provide protein domain annotation. The evolutionary epoch in which each protein was created is inferred by comparison with domain annotation of all other completely sequenced genomes. Studying the distribution across epochs of genes expressed in each cell type reveals insights into human cellular evolution in terms of protein innovation. For each cell type, its history of protein innovation is charted based on the genes it expresses. Combining the histories of all cell types enables us to create a timeline of cell evolution. This timeline identifies the possibility that our common ancestor Coelomata (cavity-forming animals) provided the innovation required for the innate immune system, whereas cells which now form the brain of human have followed a trajectory of continually accumulating novel proteins since Opisthokonta (boundary of animals and fungi). We conclude that exaptation of existing domain architectures into new contexts is the dominant source of cell-type–specific domain architectures.
Keyword CAGE
Protein domains
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
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Created: Thu, 26 Jun 2014, 21:11:09 EST by Cathy Fouhy on behalf of Aust Institute for Bioengineering & Nanotechnology