Figure 5. The set of genes bound and regulated by Pax6 in the embryonic cerebral cortex.

(A) Identification of a set of 343 genes both bound and regulated by Pax6 by intersecting the three genomics datasets reported here: Pax6 ChIP-on-chip and the array analyses of Pax6 gain- and loss-of-function cortices. The intersection is highlighted in blue (see Table S4 for details). (B) Definition of the sets of genes bound and positively regulated by Pax6 (green shading) and negatively regulated by Pax6 (red shading). (C) Breakdown of the evidence for positive or negative regulation of genes by Pax6: 23 genes show regulation following both gain and loss of Pax6 function, 42 show regulation only upon loss of function and 278 show regulation only upon gain of function. (D–F) In situ hybridisation data for cellular expression of Pax6 bound and regulated genes in whole embryos at E14.5 was available for 279 genes (GenePaint), 56 of which were not detected at this age. Blind scoring of cellular distribution of expression patterns of the bound and regulated genes (D, E) found that the majority of genes were expressed by neocortical stem/progenitor cells (VZ), including substantial numbers of genes expressed in both the VZ and in differentiating neurons, as well as genes exclusively expressed in the VZ (E). Many Pax6 target genes were also expressed by basal progenitor cells in the SVZ. Examples of genes expressed in all three cell types (VZ, SVZ and CP) are shown in F. Scale bar, 500 µm.