The roles of non-coding and protein-coding genes in the evolutionary expansion of the cerebral cortex

The diversity of brain organizations is spectacular amongst vertebrates. The greatest variations are observed in the dorsal cortex and near its junction to other structures (at the pallial/subpallial boundary). Dorsal cortex of avian and reptilian brains contains only a component of the six layered isocortex of mammals. Although fundamental structures of the isocortex are similar in all mammals, there is a drastic increase in cortical size and complexity in mammals culminating with the human brain. Comparative developmental studies suggest that the elaboration of the mitotic compartments might have been the drive behind mammalian cortical evolution (Rakic, 1995; 2006; Kriegstein et al., 2006; Molnar et al., 2006a,b). The mechanisms and genes responsible for generating these variations can be understood by studying cortical development in various different species. This proposal examines two groups of genes. (1) The first group consists of protein coding genes which are known to be involved in cortical neurogenesis, formation of layers, radial and tangential migration of neurons. (2) The second assortment includes non-coding so-called 'macro-RNA' genes that exhibit distinct signatures of purifying selection, suggestive of functionality. Using the tools of modern genetics and comparative genomics we shall sequence and compare selected groups of genes from both categories and test their function in knockout mice and in in vitro and in vivo experimental paradigms. Through the study of these coding and non-coding genes, we wish to determine, in various taxa, the context in which the most common cortical development genes operate. Comparative aspects of cortical development not only point to evolutionarily relevant changes, but they also draw our attention to the limitations of some of the model systems currently used to understand human cortical developmental abnormalities and indeed reveal the mechanisms responsible for these abnormalities.

The vertebrate cerebral cortex ranges from a 3-layered dorsal structure in reptiles and birds, to a gyrencephalic 6-layered structure in primates and other mammals. We hypothesize that slight differences in vertebrate developmental programs during evolution are responsible for the radial expansion contributing to increased lamination of the mammalian cortex and, later, for the tangential expansion of cortical surface area that ultimately produced the gyrencephalic cortex. Recent reports suggest that the origin and elaboration of the subventricular zone (SVZ) of cell division during vertebrate evolution facilitated this transition by increasing the pool of neural progenitors and prolonging the period of neurogenesis (Kriegstein et al., 2006; Molnar et al., 2006). These distinct mitotic compartments (VZ, SVZ / InternalSVZ and OuterSVZ in macaque) might enable unique and novel combinatorial effects from the available transcription factor pool. Given the high similarity between protein coding genomic regions in closely related organisms, subtle alterations within highly conserved noncoding genomic regions may have led to rapid and drastic alterations in brain formation. However, this claim remains unexplored as high quality genomic sequence and neuroanatomical analyses are available in very few species. By superimposing comparative genomic information that identifies brain-specific non-coding genes under purifying selection onto a neuroanatomical report of cortical neurogenesis in several different vertebrates, we seek to identify critical genetic and molecular factors involved in the formation of cerebral cortex with specific attention to the subventricular zone. From this template, we aim to isolate species or clade-specific brain development processes, associate these changes with alterations in particular genomic regions, and then use these observations as a foundation to reconstruct the evolution of the mammalian cerebral cortex.