Abstract
Organismal complexity broadly relates to the number of different cell types within an organism and generally increases across a phylogeny. Whilst gene expression will underpin organismal complexity, it has long been clear that a simple count of gene number is not a sufficient explanation. In this paper, we use open-access information from the Ensembl databases to quantify the functional diversity of human genes that are broadly involved in transcription. Functional diversity is described in terms of the numbers of paralogues, protein isoforms and structural domains for each gene. The change in functional diversity is then calculated for up to nine orthologues from the nematode worm to human and correlated to the change in cell-type number. Those with the highest correlation are subject to gene ontology term enrichment and interaction analyses. We found that a range of genes that encode proteins associated with dynamic changes to chromatin are good candidates to contribute to organismal complexity.
Highlights
Eukaryotic organisms show increased complexity, when considered across a broad phylogeny, but is it possible to identify specific groups of genes, related in structure or function, that make a major contribution to this feature? In this paper we take a simple, three-step approach to identify such groups
Genes involved in chromatin organisation relate to organismal complexity quantification, instead, the main reliance in recent years has been on the number of different cell types within an organism [1,2]
Genes involved in chromatin organisation relate to organismal complexity and demethylases and histone acetyltransferases and deacetylases, which are involved in the covalent modification of histones associated with both activating and repressing gene expression [22,23]
Summary
Eukaryotic organisms show increased complexity, when considered across a broad phylogeny, but is it possible to identify specific groups of genes, related in structure or function, that make a major contribution to this feature? In this paper we take a simple, three-step approach to identify such groups. As much as it is accepted that organismal complexity increases across the eukaryotic phylogeny, it is clear that the underlying mechanism will involve changes in the expression of genes that determine the formation and function of differentiated cells It was realised from an early stage in the genomic era [3], that there is insufficient variation in total gene number, from species to species, to account for increased complexity. The Encode project [7] is working towards a comprehensive analysis of regulatory elements, but there is currently insufficient information on promoters, enhancers and silencers across a wide range of species for regulatory elements to be included in this analysis It is possible, to use the annotation information collected in genomic databases such as Ensembl [8] to consider changes in the protein-coding capacity of genes. The aim in this paper, is to quantify the change in these variables for specific genes across a range of species and correlate this change with organismal complexity
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