Transcriptional and epigenetic mechanisms of early cortical development: An examination of how Pax6 coordinates cortical development

Abstract

The development of the cortex is an elaborate process that integrates a plethora of finely tuned molecular processes ranging from carefully regulated gradients of transcription factors, dynamic changes in the chromatin landscape, or formation of protein complexes to elicit and regulate transcription. Combined with cellular processes such as cell type specification, proliferation, differentiation, and migration, all of these developmental processes result in the establishment of an adult mammalian cortex with its typical lamination and regional patterning. By examining in-depth the role of one transcription factor, Pax6, on the regulation of cortical development, its integration in the regulation of chromatin state, and its regulation by cis-regulatory elements, we aim to demonstrate the importance of integrating each level of regulation in our understanding of cortical development.

Keywords: Chromatin; Epigenetics; Pax6; Transcription; cortex; cortical development.

Figure 1

A) In wild-type mice, the Pax6 protein possesses a homeodomain and a paired domain which can be subdivided into PAI and RED subdomains. The transcription factor is present in the cortex in a graded expression pattern which is necessary for appropriate cortical development. This includes the patterning of cortical regions such as motor (M), somatosensory (S), auditory (A) and visual (V) cortex. Moreover, the ventro-dorsal pallial (blue in drawing on right) and subpallial (pink) boundary is appropriately positioned. Finally, a corticothalamic projection (CTh) and Tbr2⁺ basal progenitors can be observed. Note also the correct formation of the eye in the presence of Pax6. B–E) Pax6 mutants have mutations in different subdomains (depicted on the Pax6 structure schematic) which result in a large array of cortical and ocular phenotypes (denoted by asterisks). B) The Pax6^Sey/Sey mouse has a smaller and thinner cortex, patterning defects of both cortical regions and the pallial-subpallial boundary and a loss of the CTh projection as well as of Tbr2⁺ cells in the SVZ (Hill et al., 1991; Stoykova et al., 1996). C) The Pax6^Aey14 mouse has the same phenotypes as the Pax6^Sey/Sey mouse although it is unclear whether the CTh and Tbr2⁺ cells are also affected (Haubst et al., 2004). D) The Pax6^Leca2 mutant has no obvious cortical phenotype (though the CTh projection was not described) but has some ocular defects in the form of cataracts (Walcher et al., 2013). E) The Pax6^Leca4 mutant has a thinner cortex and some ventral cortical patterning defects as well as a small eye phenotype (Walcher et al., 2013). F) Both D6-Pax6 and Pax77 mice overexpress Pax6 and have a thinner cortex, an increase in Tbr2⁺ cells/expression and a small eye phenotype (Manuel et al., 2007; Sansom et al., 2009; Georgala et al., 2011b). In addition, the Pax77 mouse has a smaller somatosensory area and retains the CTh projection (Manuel et al., 2007).

Figure 2

A central unanswered question is how are the gradients of TFs in the VZ translated into positional information in the SVZ and CP, to generate cortical regions? We hypothesize that enhancers active in the VZ {E1, E2}, SVZ {E3, E4} and CP {E5, E6} are differentially bound by TFs that drive expression of region/layer-specific genes in post-mitotic cortical neurons. The enhancers serve as protein-binding modules that translate rostrocaudal gradients of TFs in cortical progenitors into region-specific expression in cortical neurons. In this simplified model, enhancers active in the SVZ (E3, E4) and CP (E5, E6) are primed in the VZ by TFs. A filled colored box symbolizes TF binding to the enhancer; an empty box symbolizes that the TF, which is no longer expressed, had previously bound that enhancer, and modified its epigenetic state. For instance, binding of a PAX6 in rostral VZ cells (where its concentration is highest) preferentially activates rostral VZ enhancers (E1) and not caudal VZ enhancers (E2) that are activated by EMX2 and COUPTF1. We postulate that PAX6, EMX2 and COUPTF1 will prime certain SVZ and CP enhancers, marking them epigenetically with modified histone marks of poised or active chromatin, thus passing on positional information to enhancers that are active in the SVZ and CP. Propagation of the VZ protomap into the SVZ and CP is carried out by TBR2, COUPTF1, TBR1 and BHLHB5.