What does the Allen Gene Expression Atlas tell us about mouse brain evolution?

Source: arXiv


We use the Allen Gene Expression Atlas (AGEA) and the OMA ortholog dataset to
investigate the evolution of mouse-brain neuroanatomy from the standpoint of
the molecular evolution of brain-specific genes. For each such gene, using the
phylogenetic tree for all fully sequenced species and the presence of orthologs
of the gene in these species, we construct and assign a discrete measure of
evolutionary age. The gene expression profile of all gene of similar age,
relative to the average gene expression profile, distinguish regions of the
brain that are over-represented in the corresponding evolutionary timescale. We
argue that the conclusions one can draw on evolution of twelve major brain
regions from such a molecular level analysis supplements existing knowledge of
mouse brain evolution and introduces new quantitative tools, especially for
comparative studies, when AGEA-like data sets for other species become
available. Using the functional role of the genes representational of a certain
evolutionary timescale and brain region we compare and contrast, wherever
possible, our observations with existing knowledge in evolutionary

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    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.
    Full-text · Article · Apr 2014 · Molecular Biology and Evolution